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By Bob Dowie
Contributing Editor
ImportCar Magazine

Exhaust gas recirculation (EGR) has been used for years to control combustion temperature to prevent spark knock as well as control NOx emissions. For the most part, these systems were trouble-free and required service only if you were dealing with a spark knock issue, or if the valve opened too early, resulting in a tip-in acceleration stumble, or the more common, bad idle quality caused by the valve not closing completely at idle.

As emission controls got tighter, and with the advent of OBD II, things started to change. We not only saw additional driveability complaints, but we also had the check engine light (CEL) telling the customer there was an emissions failure that had to be dealt with for the good of the environment and, in most states, to pass the annual vehicle inspection. In this article, we’ll take a look at some Honda EGR issues, which have also plagued the Acura line.

We’ll start with the four-cylinder Accord engines. While there have been some reports of problems with the Civic, problems with the Accord have been the most prevalent. Driveability complaints are more common than check engine lights on these models through the ‘90s. What you’ll be faced with is a stumble complaint, which is actually a misfire at part-throttle, that’s most prevalent on initial acceleration when the EGR valve is commanded to open. It feels almost like a bad wire and happens just when you’d expect a secondary ignition problem — part-load acceleration.

The cause of the misfire is an excess of recycled exhaust gasses in one or more cylinders. The cause of this excess flow is actually plugged passages in the manifold leading to the other cylinders. When there is no flow to those cylinders, the remaining cylinders receive all the exhaust gasses, which cause the miss.

This problem has caused a great deal of frustration with techs, resulting in a lot of misdiagnosis. That’s not very surprising considering how well this problem mimics a secondary ignition problem. Then, to further confuse the issue, if there is a CEL, it’s often for the misfire and not the EGR system. Up until 1998, when the electronically controlled EGR valves were introduced, Honda looked at the EGR lift sensor to confirm that the valve received vacuum and opened, and that flow was taking place. Since the valve is opening, the ECU figures all is well there, but it’s well trained to pick up a misfire and is quick to report any problem that would hurt the catalytic converter.

Often the combination of the obvious miss and the misfire code will send techs down the wrong path. Not that there’s anything wrong with checking the ignition system, but it takes only minutes to confirm if it’s the EGR system giving you a problem and not a bad wire or plug. Simply disable the valve and do a road test.

You’ll probably get a check engine light but, if the miss is gone, you’ll know for sure that the EGR system is the culprit. But don’t overlook checking the ignition components. It’s good to know the miss is fixed, but there’s never a bad time to bring the car up-to-snuff on maintenance items. Plus, you wouldn’t want the car coming back with a bad cap, wires or plugs next week if you could’ve taken care of those items now.

If disabling the EGR eliminated the miss, it’s time to clean out the passages. The procedure differs slightly depending on the year of the vehicle. The early cars used a blind core plug to seal the manifold runner EGR port after machining. We’ve found that the best way to remove these plugs is to drill a small hole partially into the plug, and using a self-tapping screw, or tapping the hole for a machine screw and using a small slide hammer, to pull them out. Partially drilling them will allow you to reuse the plugs if no replacements are on hand. Replacement plugs are available and there’s actually a kit from Honda that includes the tools and plug.

Needless to say, caution is required when drilling or tapping. Grease up the drill bit and tap to catch as many of the chips as possible. Using a shop vac is a much better choice than compressed air to keep the area clean as you work. With the plugs removed, the blockage will be obvious and can be easily dislodged using a stiff wire and carb cleaner. Be sure to clean the entire port again to keep the vacuum running. This procedure is well outlined in service bulletin #98-074, which should be available on your service information system.

The next era of four-cylinder cars saw the plugs replaced by a plate covering the EGR channel as well as the ports. This was a big improvement that eliminates the need to drill and allows us to better clean out any carbon buildup in the channel and the ports. Accessibility isn’t a problem, but the injectors will have to be removed. To be safe, you may want to have injector seals available, but they can often be reused.

The latest of the four cylinders use a two-piece intake plenum with the EGR passages cast into the upper section. These cars don’t seem to suffer from the misfire problems of the earlier cars, but are more apt to have flow problems that will be picked up by the more observant OBD system setting a check engine light. To access the EGR ports and channel on these engines, split the intake and use a stiff wire to clean out the ports — a very similar procedure to the V6s that we’ll talk about next.

In recent years, EGR problems seem to be most prevalent on V-6 engines used in the popular Odyssey minivan, Accords and SUVs; only the worst cases will present driveability symptoms. It will be the check engine light providing the motivation for the customer, using the same enhanced code-setting criteria as the late-model four cylinders.

When Honda went to the electronically controlled sensor, they were now able to command the amount of lift, monitor the actual amount of lift and look at the MAP sensor making sure it had the expected effect on air flow. If anything unexpected happens on two trips, the check engine light will let the customer know.

The EGR passages on the six cylinders are in the upper section of the intake manifold. Some of the gaskets are reusable, but if you’re going in, the safe bet is to at least have a throttle body gasket on hand.

To get started:
1. Remove the plastic throttle body and manifold covers, and remove the throttle body, leaving the electrical connectors, hoses and cables attached. Naturally, this is a great time to service the throttle plate.

2. Remove the upper manifold with the PCV attached.

3. With the manifold off, remove the chamber on the opposite side of the manifold from the throttle body along with the intake air temp sensor, PCV hose and brake booster nipple. These are removed to provide better access for cleaning the manifold when you’re done.

4. Turning the manifold over, tape off the intake ports leaving the EGR port exposed.

5. Using a 8mm (5/16”) drill bit as a hand-held ream, clean out the port. If you’re installing the update kit, now is when you’ll drill the manifold using the bit provided; be sure to follow the cautions included with the kit so as not to damage the manifold.

6. The next step is a thorough cleaning, flushing all the ports and intake runners from both directions. If you’re doing the update, now is also the time to install the EGR pipe.

7. Finish up by inspecting the EGR port in the manifold base and cleaning as required. This is best done with the EGR valve removed.

The aforementioned update kit is fully explained in Honda service bulletin #05-026, which also details the 8-year, 80,000-mile warranty extension for the EGR system. Many of these cars have been updated, but you’ll still see plenty of them with well over 80,000 miles that will be experiencing this problem, as well as some vehicles that aren’t covered in the bulletin. Nonetheless, the bulletin is a good resource to have.

While port restrictions are the most common cause of a P0401 code, that’s not the only reason you’ll see it. With the older vacuum-controlled EGR valves, there have been issues with the vacuum-switching valves being intermittent. Testing is straight-forward. With the engine running, be sure vacuum is available at the inlet side of the valve, then hook up the gauge to the hose leading to the EGR valve.

With the electrical connecter unplugged from the switching valve, introduce battery voltage to the black/yellow wire and apply ground to the red wire at the valve side of the electrical connector. If all is well, you’ll show vacuum on the gauge. As I said, these valves have a reputation for being intermittent, so repeat the test in quick succession looking for slow or no response on the gauge.

The electronic EGR valves are quite reliable but certainly haven’t been trouble-free; the problems we’re seeing with them are more about them sticking and not doing what they’re told. The good news is they’re not hard to diagnose when you know what you’re looking at. Let’s look at the connector on a 2002 model. We have five wires that handle valve operation and reporting; the valve is power-side controlled with a duty cycle signal from the ECU through the pink wire that gets its ground from the black wire.

On the reporting side, the yellow and blue is the 5V reference signal from the ECU for the position sensor, the green and black is ECU ground, with the white and black sending the signal back to the ECU, letting it know how the EGR is responding to direction. An increase in operational duty cycle should result in a smooth increase in reporting voltage with no dropouts. Many scan tools will let you look at and log command and reporting data on a road test. Otherwise, with good access, it’s not difficult to back-probe the connector and get the same info on a multi-channel graphing meter.

We can also use what we know about the wiring to check for blocked passages and the basic operation of the valve. With the electrical connector disconnected, the valve will open by putting battery power to the terminal that the pink wire is connected to and grounding the black wire terminal. If the ports are clear and the valve is working, the engine should quickly get rough or stall, and smooth out when the valve is closed.

When diagnosing a driveability problem, it’s important to keep in mind if you have a problem on light acceleration at low RPM, when the EGR is commanded on, suspect the EGR system. Or, an intermittent rough idle may be the result of the valve not completely closing. Otherwise, the EGR system shouldn’t be suspected.

If I can leave you with one solid tip for diagnosing and repairing EGR problems on the Honda line of vehicles, it’s to check your service information system for service bulletins. Honda does a great job of making this information available to the aftermarket, and it’s just foolish not to take advantage of it. If you’re not going online, checking for bulletins and making full use of services like iATN, and OEM info like that available from Honda (, you’re just leaving too much good information untapped. The way things are going, you won’t be able to afford doing that much longer.

Bob Dowie has been in the automotive service business for more than 30 years, and his shop, Village Auto Works in Chester, NY, specializes in Honda, Toyota, Mazda and Nissan repair. Dowie owns and runs a Honda Civic and Nissan Sentra SER in SCCA GT5 racing, and gets his technicians involved in various aspects of the sport.

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