Common Problems with the E39 BMW 5-series (525i, 528i, 530i, 540i)


In terms of parts sales, a huge chunk of our BMW surprisingly (or not so much) ends up on an E39 BMW 5-series.  Built between 1995 and 2004 in the wonderfully pronounceable Dingolfing, Germany, this generation was a worthy successor to the very good E34, and was available in Sedan and Wagon with a variety of trims and engines.  This will be a generalized post, so if you come up with something that YOU’VE come across, don’t hesitate to leave a comment below to help anyone that stumbles upon this post while potentially shopping for a car, or diagnosing one they already have.  I am going to focus on the most common 6 cylinder M52 and M54 engines.  Here are some of the top problems that we’ve seen for the BMW E39 5-series cars.

E39 BMW 5-series Cooling System Parts

As with most BMW’s (for reasons we don’t particularly understand), the cooling system is one of the biggest weak points of the E39 BMW 5-Series.  Radiators crack, expansion tanks leak, thermostat housings deform, water pumps and cooling fans explode, fan clutches seize.  It’s a mess, but luckily with a little money and a weekend day you can postpone any cooling system problems before they happen.  Here are the parts you would need to bulletproof your E39 and avoid being stuck on the side of the road like so many sad drivers before you.

Before starting below, be sure to check out our ultimate cooling kit that replaces all common failure points in the E39 525, 528, and 530 cooling system, including hardware.

Radiator – The OEM factory radiators are Behr, while Nissens (an OES for other carmakers) is the same quality for a little less money.  All Aluminum options are nil, but rest easy as the OE aluminum units usually last around 80-100k miles before failure. [see parts]

E39 BMW 5-series aluminum radiator

A radiator is the main culprit for E39 BMW 5-series cooling system failures, although several other engine cooling parts are known to commonly cause breakdowns

Water Pump – The E39 BMW 5-Series came with a composite impeller water pump, many customers go with an upgraded metal impeller pump to reduce the likelihood of failure. Pair with an aluminum pulley as the pump does not come with a pulley and the stock plastic pulley tends to age poorly. [see pump] [see aluminum pulley]

Engine Water Pump (w/ Metal Impeller)
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Engine Water Pump Pulley (Aluminum)
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e39 BMW water pump comparison

Thermostat housing – on this car the thermostat housing also comes with a new thermostat and sensor, an important thing to always change when doing cooling system work. The Behr part is the same as Genuine BMW

Engine Coolant Thermostat (97C)
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Coolant level sensor – a common area for leaks, being at the BOTTOM of the expansion tank, this level sensor should always be replaced alongside the expansion tank.

Engine Coolant Level Sensor
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Expansion tank – Made completely out of plastic, and with several moving parts inside, it is recommended to replace this common weak point before it’s too late.  The Behr part is the same as Genuine BMW

Expansion Tank
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Expansion Tank Hose
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Radiator Fan Sensor – Like the thermostat, whenever doing cooling system service it’s not a bad idea to change the coolant temp sensor.  It’s easy to do, inexpensive, and a bad one can cause severe issues with the way your car runs.  There are two, one that controls the radiator fan and the other that sends signals to the ECU and temperature gauge.  The electronic ECU sensor is far more difficult to change as it is located in the cylinder head instead of on the hose. [see part]

Radiator Hoses – When replacing things like the radiator, thermostat, water pump etc, new hoses are always a good idea.  Old ones become spongy and can rupture, emptying all your coolant in seconds.  We have upper and lower hoses, of course.

Engine Coolant Hose - Upper
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Engine Coolant Hose - Lower
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Expansion Tank Hose
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Radiator fan and fan clutch – The fan clutch goes through a lot of stress throughout its life and will go bad when the car reaches its midlife crisis (that’s when you get BMW M wheels), when bulletproofing your cooling system the fan clutch should be replaced, along with the fan itself.  The fan is a plastic unit that gets brittle with age and head cycling.  If the fan clutch is wearing out and getting jerky, it can cause the fan to explode in spectacular fashion, inevitably puncturing the radiator and potentially destroying the fan shroud as well.

Engine Cooling Fan Blade
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Engine Cooling Fan Clutch
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Coolant – We proudly carry ROWE, which is made in Germany and fits all the exact same specs at a lower price than Genuine.  We also carry Genuine BMW coolant for a great price.

Engine Coolant Antifreeze (1 Gallon)
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E39 BMW 5-series Thrust Arm Bushings

Lemfoerder Thrust Arm

This control arm has a brand new bushing and ball joint already installed, just swap and go. Poly bushings are also available.

The front suspension on E39’s is designed to be the best in the business.  Part of this design has a special type of upper control arm called a thrust arm.  Also called a tension arm, this control arm effectively reinforces the geometry of the front wheels, specifically under braking.  Imagine it like the cross stay on a truss going towards the front of the car.  Liquid filled from the factory, the bushings in the thrust arm are notorious for going bad.  You do not want this, specifically because when the wheel has an inch and a half of forward and backward play, the geometry gets really sketchy under braking.  I’m talking about “toe steer”, and it can cause the car to dart from side to side when you want it to be the most stable.  We have several replacement options, including a Powerflex bushing set that carries a lifetime warranty, guaranteeing trouble free braking for the life of the car. [see parts]

E39 BMW 5-series Rear Ball Joints

Brand new rear ball joints will make a huge handling difference over worn out ones

Kind of like the thrust arm bushings, the rear ball joints take a ton of abuse, even with just normal driving.  This is because the geometry on the rear of the car (unlike many other vehicles in the same class) is designed in a way to eliminate changes in alignment, specifically toe, under load.  To achieve this required a ball joint rather than a bushing, and most cars nearing 100k miles will need these replaced.  When this ball joint is bad, you can hear clunks, feel the rear of the car wander, and occasionally squeaks as well.

Ball Joint - Rear
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E39 BMW 5-series VANOS Seals

The VANOS system on the M50, M52 (single VANOS) and M52TU, M54 (double VANOS) is a variable cam system that is driven by oil pressure. You can read more about how it works here.  It is reported that the seals in the sliding pistons within the VANOS unit go bad from being manufactured with the wrong material.  When the seal goes bad, the hydraulics cease to function and you have a broken VANOS, which will make your BMW E39 5-series run terrible.  It’s important to think about these seals and these units when you are encountering a poorly running engine and check engine lights in reference to a VANOS jam, P1519 among others.  We are working on getting an inexpensive solution to replace these seals.

E39 BMW 5-series V8 Valley Pan

M60 M62 Valley Pan Upgrade Kit

Our valley pan upgrade kit comes with a redesigned seal, as well as the other required parts you need to replace when doing this job.

This specifically applies to the V8 guys out there, and not just the 5-series.  The M60 and M62 V8 engine went in a few different chassis but they all have an issue with a seal between the cylinder heads.  Commonly referred to as the valley, there’s a pan that covers a fairly large coolant passage that travels from the back of the block to the front.  This cover came from the factory with a rather ineffective gasket, and when it starts to age coolant will seep past the seal and pool up on top of the valley pan cover.  If you notice a good sized antifreeze coolant leak coming from this area (it will smell like sweet syrup), you’re in for a big job.  The manifold needs to come off, but luckily we carry a replacement cover that has a molded rubber gasket set in it.  This redesign keeps the valley pan sealed and leak free for the rest of the life of the car. [see part]

Valley Pan Replacement Kit
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Front Struts

Contact Us if you would like us to assemble a kit of your choice, making a DIY job much easier or a shop labor less expensive. Performance combinations are available.

For whatever reason, most likely due to the strange geometry of the front suspension mentioned above, when the front struts go bad things go haywire.  Manifesting as an occasional violent shutter under braking, the front wheels get caught in a vertical oscillation resulting in significant loss in braking power in some situations. Many E39 drivers have encountered this, and it’s not something to take lightly.  We offer a variety of choices for customers looking to replace their E39 suspension, including OE Sachs (what came on the car from the factory), KYB, Koni, Bilstein, and Genuine BMW.  In addition, eEuroparts builds struts.  That means if you are a DIY’er, but you don’t want to go through the process of utilizing the dangerous spring compressors needed to assemble a strut, we can do it for you!  We have a few struts for the E39, but if you need a set of front struts that we don’t have listed on the website contact customer service.  We can get a strut assembly built for you in just a few short days so you can get it, install it, and enjoy it quickly.

E39 BMW 5-series DISA Valve/blend motor

E39 BMW 5-series DISA valveDescribed in more detail in this blog article, the Intake Manifold Adjusting Unit, also known as the DISA valve, came on many E39 cars with M52 and M54 6cyl engines.  Basically this is a plastic valve in your intake manifold that diverts air around separate passageways to improve power throughout the rev range and flattening out the torque curve.  When they go bad, they will rattle and cause sluggish acceleration, bad idle, and hesitation.  When they go REALLY bad, the flap can completely break apart and send chunks into your engine.  We’d call that a catastrophic and this happens from time to time.  If you have a high mileage car and have never changed this, it is time.  Preemptively changing the DISA valve will rule out the possibility of breaking down in the future.

Intake Manifold Adjusting Unit (DISA Valve)
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E39 BMW 5-series Window Regulator

E39 BMW 5-series window regulator upgradeIt’s quite common to get into your E39 on a nice day, go to crack the window, and get a few different results.  The first is the best, everything works fine and the window goes down.  Sometimes it doesn’t play out like that.  The window can get stuck, come off the track, or fall down into the door.  That’s a failed window regulator, which you should replace asap to avoid letting moisture into the car among other things.  The stock E39 BMW 5-Series window regulator is a little flimsy and has a few failure points.  eEuroparts caries a URO Premium unit that carries a lifetime warranty, and that’s because they build their window regulators with ball bearing pulleys, instead of the stock ones which are just plastic sleeves.  Important note, be sure to thoroughly reseal the vapor barrier (the thin foam sheet that you have to remove to get in the door), or else you risk letting water in that will cause major problems for you years down the road. [see parts]

E39 BMW 5-series Headlight Adjustment Mechanism

E39 BMW 5-series headlight head lightIf you have halogen headlights and feel like they are pointed way too low, you are not alone.  E39 BMW 5-series cars equipped with halogen headlights feature a pair of adjustment screws located on each assembly that control the horizontal and vertical aiming.  Made of kind of squishy plastic, these adjustment screws twist off or break, letting your low beam dip straight to the ground.  There are kits to allow you to replace the screw, but they all require you to take the headlight apart by baking it, melting the glue, taking the mechanism out, finding an aftermarket solution, and then gluing it all back together with an airtight seal.  This is not a project for the faint of heart, and although you will save some money expect to spend a weekend day on a project like this.  Alternatively, you can replace the headlights with brand new ones at eEuroparts.com and enjoy perfect headlights on your car once again. [see parts]

E39 BMW 5-series Ignition Switch

OEM BMW Ignition Switch

Being just the electronic portion, this part requires no programming and is not a theft related part

There are few things scarier than an aging BMW that is starting to have strange electrical problems.  Warning lights coming on and off, seats or steering wheel moving like they are haunted, radio malfunctions, climate control funniness.  You don’t have to take your car in for an excorism (yet), many other e39 owners have encountered similar problems and fixed them with a new ignition switch.  We sell a ton of these, so this happens quite a bit.  The switch itself is not too expensive or difficult to remove, so if your E39 BMW 5-Series is acting like it’s haunted, chances are a new switch will cure it.  eEuroparts.com carries the E39 ignition switch in a few different brands, we recommend the Made In Germany Febi unit or the Genuine BMW part.  To replace, you have to remove the black plastic clamshell around the steering wheel, the switch is held in underneath with a few screws.

Ignition Switch
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Bonus Round

Even with the common stuff out of the way, like any car you will have to replace other parts as time goes on.  Luckily we have nearly everything you could ever need or want for your E39 BMW 5-series, from brake kits to oil changes, side mirror covers to alternators, head gaskets to air filters.  Hit the jump below to put your specific E39 BMW 5-series into the vehicle selector and start shopping for things to get your fine German executive car up to full speed in the luxury you deserve.

E39 BMW 5-series Brake Kit

[Shop E39 BMW 5-series parts]

17 thoughts on “Common Problems with the E39 BMW 5-series (525i, 528i, 530i, 540i)
  1. Sheryl Lee

    2001 BMW 530i check engine light comes and goes on the dash board. Diagnosis: smoke test performed: engine leak fix that problem light came back diagnosis code : catalic converter. Mechanic said not a problem
    Need help

  2. ghazwan saeed

    please I have Bmw E39 Model 2000 got a problem in the dashboard. It does not read the faults in the car, such as burning lights or if the door is open. Knowing that the screen is working properly.
    (( There is no warning of malfunctions ))
    Please I tried all the sites and did not get the correct answer and please help me solve this problem
    thank you

  3. Seun

    Pls I’m having problem with 1999 e39 BMW car.I had changed the master break, the hose,the calibers still the same problem. It will act normally when it’s not hot but when it’s hot it will not free and the break will not be active anymore. I thank you

    • Adam Goral

      It’s hard to say what is wrong with this description, but I do understand that you have a severe issue with your braking system and it should be diagnosed by a professional. Please find a local BMW shop and have them take a look, they will use a variety of special tools to accurately diagnose your problem.

      • Jeffrey Oswald

        Are rubber flex hoses fitted to these cars? I had an awful and under-maintained Volvo once, where if one (or three) of the calipers wasn’t hanging up, the flexible lines had broken down internally to where they functioned as one-way valves. Brake fluid pressurized the caliper, but it would not release. Worst car ever.

      • I have a 1997 BMW 528i that i can not very to start. It will crank but not start. I took the batter to auto zone and had then fully charge the batt . i put gas in it and the fully charged battery in. Still did not torn over. Did OBD2 reader came back crankshaft sensor. So i replaceed that and the ignition switch and still nothing. Can someone help me please?

        • Adam Goral

          Please take this car to a mechanic that has access to the diagnostic tools to accurately find the problem here. It would be nearly impossible to correctly diagnose an issue like this over the internet.

  4. Well where do I start. I absolutely love this car. Beamer, when first came out, everyone wanted one and they were pricey, like 20k brand new from dealer. Now u can find one for 3-6k and in very nice working conditions depending on who you get it from. I would love to find a low miles m5. But still I heard lots of problems these cars, therefore if you are not a mechanic or don’t have a lot of money, then you might not want to get yourself into this mess and hope to have a reliable daily driver. Stick with Ford.

  5. Timothy Harris

    My 2000 e39 have had some of those problems but if you address them in a timely manner it not that bad to replace them and not to expensive. My girl is 19 years old know and I love her same as the day I brought it BMW forever for me.

  6. Hey guys,
    I am under way of completely renovating the mechanics of BMW533i w/ m30 engine. I get the engine from machine shop next week so i need a article of the most common problems to watch for & other advise or upgrades or precautions to be aware of specific to the M30 engine.
    Great prices I need to make another order.

  7. Alan

    The weak cooling system is due to them running the engine coolant at 230F all the time. I have a E39 540i 4.4L and just did an overhaul (refreshening of the engine: Vanos, Chain Guides, valve cover seals, etc.). At 110K all of my seals were rock hard, which typically happens when you bake them all the time. Those high temps are also not good for long term durability of hoses and plastics. Do yourself a favor and get a lower thermostat down to around 190-195F. Unlikely you will have a cooling system failure for a long time or valvecover oil leak. Some will argue that bmw designed it that way for a reason. While true, it is not always in the best interest of the customer as there are competing tradeoffs.

  8. I have a 2001 BMW 530 series. When I bought it I could smell oil But I was coned into thinking there was nothing wrong. I had it checked and I was told it was a very small leak. A few minutes later it started smoking really bad and it tried to die on me. My problem is I didn’t drive it very much. I had a second vehicle. So when it did this I managed to pull in Walmart where they work on cars. I had the oil changed. They didn’t want to do that. No one around here works on them. I managed to get it home but it kept smoking and I managed to get in my driveway. Since then I’ve had it boosted off and we drove it down the highway & back. I’m just afraid to try going anywhere in it because I don’t want to get stalled. But when it was running, it ran great! But you could smell oil really bad!

    • Mark Goodson

      Change your crank case vent valve on the back of the intake manifold. Its a little tight but there are 4 or 5 5mm allen bolts that hold it on. When it goes bad it sucks oil up from the bottom of the valve and into the intake, it’s normally sealed between the two, and you will look like a James Bond spy car putting up a smoke screen!!

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