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Common Problems and Fixes

These are great cars, but they have their share of problems. Major components seem relatively solid; however, there are many mostly smaller issues that are common.

Below is a list of some of the typical problems seen in these cars along with causes and fixes. This is not intended to be a comprehensive list; rather, it's simply a list of those problems which seem to affect almost all of these cars. Most of these are recognized issues that affect all E39s. None are specific to the 6-speed as far as I know, and very few are specific to the 540i versus the other models. Many are at a frequency that they probably should be considered production defects by BMW.

Problems that I've personally experienced, I've marked with an asterisk ( * ).

If you know of others that should be listed here, or can provide links, pictures, or fill in TSB or other fix info, please e-mail me.

Service manuals now are available from Robert Bentley. It's a two-volume set that retails for $169. Available through Amazon for about $50 less with free shipping. See Bentley's detailed description.

There now is a paid "official" on-line source with the ETK (parts) and TIS (service information including TSBs) available here: Unfortunately, access is relatively expensive (currently $20 per day or $200 per month currently).

The approved source in the US for printed technical documentation, software, and service bulletins from BMW is Central Letter Shop in Fairfield, NJ. Information available (for sale) includes:

  • TSBs in printed format; and
  • software available on CD, including the TIS disk which provides TSB/SIBs, technical references, and service/repair instructions.

There also are many "unofficial" sources for the ETK, TIS, and other CDs.

Alldata has online listings of the titles (only) for TSBs and recalls for:

The National Highway Traffic Safety Administration provides searchable online databases for recalls, TSBs, and consumer complaints at the following sites:

Common Problems Experienced with E39 BMWs
Radiator failure*

The radiator cracks in the area where the upper inlet hose joins the radiator. This probably should be considered a design/ manufacturing defect (but good luck arguing that).

Most common on the 540i, and does not seem to be a frequent failure on the I-6. See the results of a recent informal survey regarding this problem.

Replace radiator. No standard source for an all-metal replacement as far as I know.

For replacements, check with your dealer first. Pricing was reduced recently (10/02) and OE radiators now are avaialble for under $200. Aftermarket pricing should follow, so the pricing information below should change for the better.

Behr OEM replacements, with a lifetime warranty and best-price guarantee ($250 - $358 at last check), are available at

Note that pricing across model years from is all over the board. Apparently, there are physical differences between the pre-8/98 version (26") and the 99 (25"), and also between 2000 and 2001. Also, there are several options within years (one-row and two-row, etc.) that aren't reflected on the web site.

Behr ($294) and Nissens ($258) are avaliable with a one-year warranty at

Rebuilt units with a one-year warranty are available for probably about half of that at Reseda Radiator if you want to go that route.

Zionsville now has an all metal version. Expensive at ~$650 but might be a way to go if you plan to keep the car for an extended time and don't want to have to worry about it again. I've not tried these myself so I can't say as far as fit or function. I've not seen any problems posted.

Also consider changing the expansion tank at the same time since they seem to follow shortly after problems with the radiator.


Water pump failure*

Water pumps tend to fail relatively frequently in older models (within 50K miles). Plastic impellers are often cited as a cause; however. none of the original up to at least 2001 E39's should have the plastic impeller. (Mine did have plastic, but it may have been previously replaced).

Another cited cause is loosening of the water pump hub nut on the front of the pulley which drives the pump. If loose, it allows play in the pump resulting in wear. (This was the primary cause of failure in my case.)

Pump bearing failure also is cited as a cause and seems much more common in the case of the V8 than the I-6 models.

Replace water pump. Best to use a metal impeller. Later models and all new pumps have metal impellers.

I've heard recently that BMW now is using an "improved" plastic impeller again in some models. The only reason to use plastic is to shave costs over many units. Get the metal if possible.

  Coolant low messages from MID*   Coolant level below acceptable range.  

See TSB #17 01 01.

Also check sensor at bottom of expansion tank.

Make sure that you don't have a slow leak in the system.


  Misc. coolant leaks*  

Coolant leaks toward rear of engine.

Also, leaks from bottom of expansion tank.


Check for loose or deteriorated hoses or tubes where heater inlet/return are located at the firewall toward driver's side (remove plastic engine cover for a better view). Tubes between the cylinder banks and the valley gasket also reported as potential sources. Expansion tank tends to leak at the lower fitting and under where the sensor attaches.


  Cam shaft position sensor failure*   A common cause for check engine lights. Engine may run rough and hesitate.

Independent of actual failure, water in the engine compartment (e.g., washing the engine) sometimes can trigger this fault.

Replace cam shaft position sensor (part number 12-14-1-742-185) and reset fault memory.

If engine recently was wet, let dry and light may go off after a few starts.

Also for check engine light on, make sure that the gas cap is on tight; however, this seems rarely to be the actual cause.


  Power steering fluid leaks*  

Leaks from PS reservoir cap or from hoses/fittings are common.


Identify source of leak working top down from the PS resevoir cap.

If leaking from the cap, replace the
small o-ring (part # 32 41 1 128 333) at the base of the threads on the cap. Look very closely, it's hard to see. Note that even after replacing the o-ring, mine still leaks at the cap. A larger gasket would be better.

If leaking from hose, replace hose/fitting and o-rings. Check at bottom of radiator on driver's side.


  Valve cover gasket leaks*  

Oil seeps from valve cover gaskets, usually to the point that oil accumulates in the plug wells. Small leaks generally aren't a real problem.

Almost exclusively a V8 problem.

  Replace valve cover gaskets.  
Drive train
  Front wheel bearings   The front wheel bearings are considered by some to be of rather marginal design, particularly if used with larger wheels and/or brakes.  

Some say replace with updated bearings (same part number, but updated design), or substitute M5 bearings (different part number). The latter requires some modification to accommodate the index "bumps" on the M5 bearings. See Dave Z.'s excellent page on R&R for E39 front wheel bearings.


  Rear tire wear excessive*  

Will very quickly wear the inside edges of the rear tires unless proper alignment is maintained. Weight in the rear tends to increase the effect.

  Regular alignment using quality equipment. Correct rear camber for the 540 is in the range of -2.2 to -2.0 degrees.  

  Front end "shimmy"  

Multiple causes including wheel balance, bent wheels, low air pressure in front tires, bent rims, worn front-end bushings, too "pinched" of an alignment, etc.


Usually fixed by standard process of elimination. Some cars seem plagued with very difficult to resolve problems.

Beyond typical tire and alignment checks:

Some improvement
reported by torquing wheel bolts to 88 ft. lbs. as now specified by BMW versus the earlier 78 ft. lbs. spec.

Increase front tire pressure seems to help.

Some success from replacement of the thrust-arm bushings, or the entire thrust-arm (with new bushings and ball-joints).


  Parking brake doesn't hold*   Parking brake does not hold on moderate slopes. Usually worse in the reverse direction. More noticeable with manual shifter.   You can try tightening the front parking brake adjustors. When you've finally satisfied yourself that this doesn't really work (which it won't), do it right and adjust at the rear. The front controls the position of the lever and number of clicks more than anything else.

For detailed instructions, see another excellent set of instructions for accessing and adjusting the rear brakes by Dave Z.

Also, you may find that the shoes are heavily glazed. You can improve the hold by roughing the pads a little.

BMW recommends lightly applying the parking brake while driving slowly now and then to clean the faces of the shoes and drums.
  Auxillary fan fires   Although not affecting earlier models and few 540s, this probably is worth noting first because of the potential consequences.   Contact your dealer if you're not aware of this issue and have a later model year E39.  

  Auxillary fan not working properly  

Auxillary fan does not operate as expected.

Note that there have been multiple versions of the fan, with updates issued for some used as replacements early on. Excessive noise was a common complaint with interim versions. Applies mainly to later model year cars.


See auxillary fan testing and R&R instructions.

Cost for a new fan is about $350.


  ASC light stays on   ASC indicator light stays lit regardless of switch position or driving condition.   ASC cable broken or ASC rotational sensor not functioning or disconnected.  

  Display reports check bulbs front or rear, yet bulbs working*   Bulbs are monitored by the onboard diagnostics. Corrosion on bulb base or a bulb that has resistance higher than spec may cause fault.  

Clean bulb base. Use good quality bulbs with a non-corrosive base. Check contacts and fit within socket. Replace marginal bulbs.

Brake and tail lights are reported separately, so that helps to narrow things down some.

If brake light reported, check third brake light bulb which frequently is overlooked. Brake switch at pedal also controls some of the connections to the rear.


  Display reports check fog lamps, yet fogs working*   As above.   As above.


  MID lights "flare" to bright*   Software problem in the MID.  

Replace MID. If not under warranty, live with it, or bend over and grab ankles. (TSB 62 08 99 - applicable to production date 1/2000, see TIS 65 81 010)


  Odometer and other LED display elements missing pixels*   Display for the odometer and other information appears broken up.  

Recently (4/2003), BMW has been working at an individual level to address this problem. Contact:

Lacking that, replace cluster on your own. Not too difficult to do yourself, but you must have a dealer reset odometer.

Cost for new cluster at dealer runs $650 - $850.

Repair also possible through independent VDO repair shops. See (US and international repairs) and (UK and outside the US).

Used clusters are available from:

Ken Bakers Originals
South Carolina
$300, 30-day warranty

$350, 30-day warranty

Zionsville Autosport

Consensus from those who have fixed this themselves is that the problem is bad contacts for the LCD panel which are relatively easily repaired, but cluster internals are very difficult to access.


  Battery failure  

Often, can't blame this one on BMW... typically, it's operator error. The battery is in the trunk - out of sight and out of mind. Even though it's "maintenance free" water levels need to be maintained. There tends to be a rash of BMW battery failures at the end of the summer after significant evaporation due to the heat.


Regularly check and fill the battery to proper levels with distilled water. I check mine at least once a year and usually find that it's down about 6 to 8 oz. A sports bottle with a flexible drinking tube is the best thing that I've found for adding water.

See Viet's detailed maintenance instructions.

If it fails, substitute an appropriate vented battery. Dealer price is about $300. Douglas is OEM (#49-675) and about $90. Interstate MTP-93 (add vent kit), Sears Diehard International, and others are under $100


  AM radio reception poor*   Inability to receive AM radio stations.   Supposedly, there is a booster available from dealer; however, this may not be the case. Mine knew nothing about it. (TSB 65 06 97, November, 97.)

A frequent cause of this is a loose connection on the existing antenna amplifier located in the rear C-pillar, or failure of this amplifier.

  Window actuator failure*  

Single window fails to open or close properly.

  If motor in the door can be heard, likely to be the actuator. There's a mechanical cable stop/catch that typically becomes deformed allowing the stop to slip past the catch or otherwise breaks. Replace actuator. For instructions, see:

If no motor sound, likely a switch problem. Beyond obviously checking fuses and testing individual window and door controls, the driver's control serves as the master for the system and many problems seem to be there.

Note that the driver's window also can malfunction and appear inoperable depending on when the switch is hit when entering and starting the car. Turn off and try again.

  Door actuator failure  

Single door fails to open with remote activation or very noisy. Opens with key.

  Replace actuator. For instructions, see:

  Trunk actuator failure  

Trunk fails to open with remote activation or very noisy. Opens with key.

  Replace actuator. For instructions, see:

  Sunroof or windows do not fully close with one-touch close*  

The sunroof or windows do not completely close when the one-touch or sometimes manual close is used.

  Reset sunroof or window by holding down the close switch button for approximately 15-30 seconds; otherwise, check for mechanical failure.  

  Fuel sender failure  

Fuel gauge shows empty with gas in tank. Often intermittent failure.

  Replace fuel sender.  

  O2 sensor failure  

Check engine light with lambda sensor as error. Four total - one pre- and one post-cat each side.

  Replace O2 sensor. See kowached's detailed instructions for replacement.  

  Outside temperature reads -40 degrees (or other obviously incorrect number)*  

The outside temperature sensor is disconnected or not functioning.

  Reconnect or replace outside temperature sensor (a small, inch long black rod under the front bumper to the right of the passenger front tire... can't miss it). It may take a day or so for it to recalibrate after reattaching/replacing. As long as it's changing, you're OK.  

  Intermittent interior heat/AC fan operation, or inability to change fan speeds, or fan runs even with ignition switch off*  

Final stage unit failed.

  Replace Final Stage Unit, part # 64 11 6 929 486, at under $100. Relatively easy fix. Unit is located under the center of the dash. Access from passenger side. See here for instructions.  

  Misc electrical gremlins*   Various electrical components not functioning or functioning intermittently.   Hang chicken foot from rearview mirror. Perform voodoo chant.  
Catalytic converter failure*
High failure rate for converters, typically within 50K-60K miles and sometimes earlier. Exhibits rattling in the exhaust and/or loss of power. Engine revs poorly. Power loss from blocked cats.

Replace under warranty (the extended emissions warranty DOES apply), or look at it as an upgrade opportunity and replace with an after-market high-flow cat at less than 1/3rd the cost, e.g., Car Sound or MagnaFlow (same, but MagnaFlow polished and slightly higer cost) , 2 1/4" inlet/outlet "no air" option @ about $65 each. See the Car Sound web site.

  Creaking or similar noises from under car when parked after driving   Exhaust cooling and contracting.   Normal.  
  Paint chips easily, especially along nose and hood*  

Paint along the front area of the car tends to easily chip and become "sandblasted." Legend has it that it's because German environmental law requires use of a water-based paint (but Mercedes doesn't seem to show this effect nearly as much.)


Some cover with 3M or equivalent film to prevent.

A color-matched filling polish/wax can be used to hide.

Typically, too many for touch-up paint, but the Autosharp Pen is popular and works well based on my experience.

Repaint if required.


  Windshield pits easily*  

Windshield becomes "sandblasted" rather quickly as a result of relatively soft glass used.

  Replace windshield. Possibly polish to minimize effect. Maintaining greater distance behind leading traffic also may help this and the above.  
  Doors make a creaking or rattling noise*   This is one of the most annoying things about these cars. The outer edge of the door seals rub against the frame of the car with every little flex and movement of the body, making an incessant light creaking/rattling noise. Slightly cracking the window eliminates the noise. (See SIB 51 03 97.)

Other sources of noises are door clips (squeaks/creaks), and weatherstriping (squeaks), and various loose parts (rattles).

Also see window clunks below.

See here for my experience regarding an effective solution for this problem.

Other than the above, you can temporarily reduce the noise by lubricating the seals with Gummiplege or other similar lube, but that gets old real fast and often ends up making it worse in the long run. Seals should be replaced with latest versions (third-generation at last count), but eventually these also will become noisy as they wear and are contaminated with dirt, wax, etc.

The key seems to be to keep the lip and corner of the seal off of the door frame, however you choose to do it. Doors that are loose and/or improperly aligned may contribute to the noise.

A few winds of tape around the cylindrical door catch may help with the "clunk" noise going over larger bumps.


  Seats click and/or rock when turning, stopping, or accellerating*

  Bushings under seat worn, loose, and/or not lubricated. Possibly, problem with seat rails.   See my easy test/repair for bushings. For more extensive information and repair instructions, see Lefty's write-up for seat removal and bushing repair.


  SRS light on*  

SRS indicator light on reflecting an error in the monitoring of the SRS system.


Due to the importance of the SRS system and the range of problems all reported by the light, really need to have the codes read and any errors properly diagnosed. Several different versions of the system are used and error codes vary across these versions.

Problems with the passenger-side occupancy sensor are very common. Requires skinning the seat and replacing the mat and possibly the control box under the seat.


  Seat belt warning light stays on even with seat belt latched*   Microswitch in driver and/or passenger side seat belt clip failed.   Replace seat belt latch to version with updated microswitch. TSBs indicate that this has no effect on operation of the air bag, but reportedly, if deployed, the airbag may be released at full force since the system detects no seat belt in use. Updated seat belt latches are marked with the date as 01.09.1997 or later. (SI 72 04 96, 6/2000.)  

  Glovebox fails to open and/or falls off hinges*   Glovebox is mounted on two adjustable large-headed bolts that rotate on a rod and act as hinges. The bolts loosen over time and allow the glovebox to slip out of alignment and/or or come off of the hinges.   Realign glovebox and tighten hinges. To open if stuck closed, pull to either side while releasing. Worst case, pull panel under glovebox and loosen adjusting bolts fully to release the bottom of the glovebox and allow it to be removed. A little Locktite on the adjusting bolts/nuts will help keep them from loosening again. See glovebox repair instructions here.  

  Cup holders front and/or rear not functional*   Cup holders jam open or closed.   Remove, step on, toss. Replace with same part or blank cover for front (I *think* 51 16 8 160 136, but confirm that) and storage bin for rear (51 168 159 701).  

  Wind noise from sunroof area excessive*   Some noise is normal. Sometimes gasket is slightly out of place or worn.  

Reseat/replace gasket if truly worn; otherwise, normal. Closing inner cover will minimize noise.

To test if seal is source of noise, tape over the edges of the sunroof and over the seal. If noise is not substantially reduced, look elsewhere.

Check that lifting pads (part number 51 71 8 204 244) are in place if noise seems to come from front of the car at the top of the windshield (SI 41 03 96, 11/96)


  Window "clunks" and/or rattles when rolled down   Window stop out of place. New stop design as of 2/98 production.  

Replace window stop with new design (part number 51 33 8 257 714). (SI 51 01 98, 5/98)


  Seat and wheel position adjustment not working   Inability to adjust seat and wheel, or wheel does not move from exit position   Usually fixed by turning off then back up to a few times. If still not working, let car sit turned off for 1/2 hour. Usually starts working again. Can be caused by hitting the seat buttons as you exit the car, resulting in a software error.

On cars post 9/98 production date, also can be caused by motor/controller communications problem. (SI 32 02 98, 7/99)

  Center air vent not moving fully through range of adjustment   Center air vent jams or is difficult to move.   Replace with updated part.  

  Interior door handles break   The interior door handles look like metal but actually are made of plastic and break either as a result of fatigue over time or force.   Replace with same part. No metal replacements as far as I know. Some early model year cars had metal handles, but current part numbers are plastic.

I was told that the M5 handles are metal and will work, but I've not confirmed this. They are significantly more expensive.

  Clicks from B-pillar in area of the upper seat belt retainers*   Excess play at the retainer for the belts allows them to tap against the plastic.  

Replace spacers with updated part number 72 11 1 978 983. (Reference TSB 72-01-01).

See Viet's page for very good DIY repair instructions.

Ticks from the plastic sliding mechanism of the adjusters also can be quieted by padding with a small piece of adhesive felt.

  Rear floor wet   Drains in door clogged and/or vapor barrier not completely attached (often after work done on rear door). Design of the interior of the rear doors causes water to drain toward the inside of the car, and with the vapor barrier out of place and/or drains plugged, into the car.   Clear drains at lower door edge and/or reattach vapor barrier.

  Steering wheel creaks/groans/squeals when turned*   Slip rings inside steering wheel housing worn and rubbing.   Replace slip rings with part number 32 31 6 759 546. (TSB 32 03 01, 10/2001)



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Copyright © 2002 by M. Andrews. All Rights Reserved.

The information presented on this site describes modifications that I have made to my car.
Should you choose to attempt any similar modifications, you do so at your own risk.

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