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Fixing EGR blockage leading to DTC P0401 and P1491
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What is EGR and why do we have to put up with it?
Photos of how Delbert Brecht fixed his annoying EGR blockage in his D16Y5 engine
A text narrative of how he did it

What is EGR and why do we have to put up with it?
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The acronym EGR stands for Exhaust Gas Recirculation. EGR is intended to reduce oxides of nitrogen in automotive exhaust, but seems mostly to cause headaches and baldness for those who have to service EGR installations.

The concept and execution of EGR is abundantly documented and easily obtained via any Internet search engine, so I won't go into much detail on it. I will say that
  1. Hydrocarbon fuels (such as gasoline, propane, butane, diesel, kerosene, Jet A, etc...) cannot combust without oxygen
  2. A spark-ignition internal combustion engine's intake charge consists of gasoline (hydrocarbons) and oxygen
  3. If certain fuel/air mixtures and/or combustion conditions should exist, emissions of nitric oxide (NO) -- or oxides of nitrogen (NOx) -- will exceed Federal regulations
  4. EGR is a relatively cheap, easy way of reducing the tendency of an engine to produce excessive NO/NOx.

The purpose of EGR is to reduce combustion temperatures by displacing some of the oxygen-laden intake air with with a gas that does not contain significant oxygen. Reduced fresh-air flow also means reduced fuel delivery, and thus less caliente combustion. You could also do this by plumbing into the intake a canister of argon or some other inert gas, but that would be bulky, complex and expensive. At least, it would be compared to simply re-routing some of the engine's own spent gases back into the intake, which is what EGR does. Those spent gases do not contain significant oxygen. Ambient air contains 21% oxygen, 78% nitrogen and 1% trace gases (which includes about 0.04% carbon dioxide). Exhaust gas contains about 0.5% oxygen.

The problem is, exhaust gas naturally contains soot, water and oil. These combine to form deposits (hard carbon) that plug up the EGR system, increase emissions, cause the engine's computer to set error codes, turn the Check Engine light on and make you wish you'd bought a bicycle instead. Most cars with EGR will eventually have a tendency to suffer EGR problems, some bad enough to warrant the issuance of a Technical Service Bulletin (TSB) by the automaker. Here's an example of one.

Honda has specific descriptions for OBD-II DTCs (Diagnostic Trouble Codes). The descriptions explain exactly what is meant by "P0401", etc. You may find a list of those codes that are valid up to Model Year 2003, here.

Former Honda technician Delbert Brecht has kindly submitted his own enlightening experience in solving the EGR blockage in his 4-cylinder '98 Honda Civic HX D16Y5 engine and manual transmission. It's detailed below. I've never had to work on EGR, and neither of our cars have it, so Delbert's submission was an education for me. By the way, V6 cars are rather more complex to fix than fours. Delbert therefore had a (relatively) painless task ahead of him. Pity the poor V6 owners...

Photos of how Delbert Brecht fixed his EGR blockage in his D16Y5 engine

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EGR valve and fuel rail, assembled
This is actually Delbert's last photo, with everything back together again, so the EGR valve you see at far left is brand-new.

I figured this was as good a place as any to start.

I'll show and describe to you the photos Delbert took, just so you have some sort of visual background on this, then I'll let Delbert take over with his narrative.

The fuel rail is the shiny aluminum bar at the back. The four injectors are immediately in front of that.

These photos are taken from the vantage point of you standing at the car's front bumper and looking down at the engine.

Fuel rail parts
These are the engine-end parts of the Civic's fuel delivery system. The unlabeled black thing to the left is the purge switching valve for the fuel evaporative emissions system. Honda used a fuel rail as a mounting point for the valve; the valve does not interact with the rail.

The EGR valve itself
This is the EGR valve itself.  It's just a variable gateway: It lets some exhaust gas into the intake, or a lot, or none at all.  It all depends on the signals received from that electrical connector at far left. Engine intake vacuum is expected to do the actual work of pulling exhaust gas into each cylinder.

The EGR valve sits on top of the thing labeled "EGR valve inlet" in the next photo.

New EGR gasket on intake manifold
As we peek behind the valve cover at the top of the intake manifold, we see that the fuel rail, injectors, EGR valve and EGR Chamber Plate have all been removed. This exposes the sheet metal gasket that's sandwiched between the EGR Chamber plate above, and the EGR portion of the intake manifold below. Small holes are let into the gasket. These holes communicate with the Chamber Plate to distribute EGR gases to each cylinder.

Delbert has stuffed crumpled paper towels into the injector holes in the intake manifold. This to keep dirt out when the holes are open..

The large hole to the far left of the gasket is the EGR outlet hole into the Chamber Plate. It allows gas to flow from the EGR valve into the Chamber Plate atop that gasket. The smaller holes in the edge of the gasket closest to you are the feeds for each cylinder from the Chamber Plate.

And that's a new gasket you see. The old one was thoroughly black with carbon.

Intake manifold EGR passages and ports
We remove that gasket, the intake manifold ports themselves are now visible. These ports also plug up with carbon and must be delicately cleaned with a drill bit (see Delbert's text further down this page).

EGR plate that sits on top of the manifold
This is the EGR Chamber Plate, shown here upside down. It sits on top of the metal gasket in the previous photo. This serves as a "distributor" for exhaust gas: It makes the output of a single EGR valve available to all the cylinders.

Gas flow is from the EGR valve outlet at far right (on the left when installed) to the large open space in the middle, then through each of the convoluted runners ("Chambers") to each cylinder's port in the intake manifold. The small numbers you see are each cylinder's, from timing belt end to distributor end.

EGR plates: dirty and cleaned
Above I showed you a clean Chamber Plate. At the top in this photo is the Chamber Plate before it was cleaned. Every single part of the EGR system is subject to carbon buildup, and it all must be cleaned off to ensure proper gas flow.

An exception to this rule is the port which communicates exhaust gas from the exhaust side of the head to the EGR valve on the intake side. It is of sufficiently large diameter that it's unlikely this will ever become occluded; the problems start at the EGR valve itself.

Delbert's text narrative (with minor addenda from me)
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I started by replacing the EGR valve and its gasket and cleaning the pipe leading to it from the exhaust manifold. I could not probe the hole at the base of the valve leading toward the intake. Dead end. Once you see the design of the interior you will understand. Although this replacement of the valve did make the P1491 code set less frequently, it still showed up on occasion. In retrospect this is not where I would start as the part is fairly expensive ($113US).

To fix the problem required removing the carbon deposits from the passageways that lead from the EGR valve to the intake manifold. Using a probe to clean them is not feasible. One must remove the fuel injection rail and injectors and a small plate called the EGR Chamber Plate. This plate has a maze like pattern of runners cast into the underside. There are four main runners that lead to four holes in the intake manifold which also must be cleaned of carbon. It is held in place with 6 bolts with sealant on the threads and has a specialized gasket made of metal and a rubber like compound.

This is for a Honda Civic HX MT [manual transmission]. The EGR valve is slightly different for an automatic. The MT valve is all electrical with the solenoid built into the valve. The automatic version is vacuum driven and has a separate solenoid to control the vacuum. The engine is a D16Y5 VTEC-e engine. I would guess that this is not the only engine that uses this type of set up.

To tell whether your engine could be repaired by this method you should look at the parts diagram for the intake manifold for your specific vehicle. If it shows an EGR Chamber Plate then the fix is similar. Here is a link to some Honda dealers that sell online parts:
Some of these dealers have parts diagrams online. Find the diagrams for the intake manifold parts and you'll see the EGR system. Not all cars have EGR! If not, you're lucky.

Parts you need (may vary by model):

Tools you may need:

Procedure to remove fuel rail, injectors and EGR Chamber Plate

WARNING: You MUST be VERY clean while handling any fuel-system components! Wash your hands or change gloves often.  Do not allow even the tiniest speck of dirt to fall into the fuel injectors or fuel rail. The factory goes to excruciating lengths to exclude dirt from your car's fuel system. Don't be the one to defeat their efforts. Dirt is a mortal enemy of fuel delivery systems.

WARNING II: Some of the photos and diagrams linked in the text below are NOT from the '98 Civic HX's D16Y5 engine, but from other engines. Your engine may differ slightly but importantly from any of the photos or diagrams in the text below. Use the text below as a guideline only, and alter it as necessary for the particulars of your car. It is always best to have a good shop manual before beginning work. The best ones are found here: http://www.helminc.com.
  1. Release pressure in gas tank but leave cap on loosely. It is a good idea to have a fire extinguisher that is functional at the ready. DO NOT SMOKE. NO OPEN FLAME OR POSSIBILITY OF SPARKS.
  2. Remove the negative terminal of the battery.
  3. Remove the connectors to the fuel injectors (4 of them) by pressing the sides and wiggling them loose while pulling up. Honda uses a variety of ways of holding these in place. These just have two tabs on the side that you push in and then pull. Be VERY careful! The connectors can be fragile! Some engines' injector connectors have a wire bale that must be pushed aside before the connector can come off.
  4. Hold the hex on the fuel filter below the banjo bolt with a wrench. Lay a shop towel around the top of the filter to catch leaking fuel. Use a second wrench to loosen the banjo bolt while holding the lower wrench steady. Remove the banjo bolt and 2 washers. Use sudden quick movement to break the bolt loose.
  5. Remove the plastic shroud that houses the injector wires and the EVAP purge control solenoid valve wires by pushing on the two tabs on the back side and pull the cover toward the back of the engine. When it is loose, lift it up slightly and disconnect the EVAP purge solenoid valve connector.
  6. Remove all the rubber hoses that connect to the fuel rail: Two on the EVAP purge control solenoid valve, one small and one large on the fuel pressure regulator,  and the PCV hose (wire or zip-tie it up out of the way).
  7. Remove the two nuts on the back side of the fuel rail which hold it all in place. They have yellow factory marking paint on them. This paint is applied by the Quality Control inspectors to indicate that the fastener has been properly torqued to spec.
  8. Slowly pull back on the fuel rail trying to bring the injectors with it. On my engine the rubber hose with the banjo fitting is "permanently" attached to the rail and a helper can feed that out of the maze of hoses as you lift the rail clear of the engine. Make note of the routing of this hose so you get it right the first time on reassembly.
  9. Using Wite-Out or similar marking substance, put  1, 2, 3 or 4, dots on the injectors so they get reinstalled in the same position they came from (this step is optional). Twist and pull on the injectors to get them out of the rail. Wipe the injector nose clean of carbon but don't mess with the needle inside the nose.
    Watch out for little wire filter baskets that fit down inside the top of the injector! If they come out or stay inside the fuel rail, retrieve them, clean them with spray throttle body cleaner and put them back in the injector.
  10. Remove the "O" ring, cushion ring and seal ring from the injector. The seal ring may still be in the intake manifold. If it is remove it, then plug up the hole in the manifold with a wad of clean paper towel so you don't drop anything in the intake. Be careful not to push external dirt into the hole while doing this.
  11. Do not reuse the old injector seals. A new set is less than $30, which is not worth saving just to risk a fire later on. Coat the new "O" ring with clean engine oil (do NOT use ANY other substance!). Slide the new cushion ring in place and then install the new, oiled "O" ring, in that order. With a twisting motion reinstall the injectors into the fuel rail.
    Don't pinch the "O" ring or it will leak! It takes a fair amount of force to get them in. Check carefully with each injector to make sure the O-ring isn't being pinched. You can use your fingernail or other blunt object to try and help it go home. The new seal rings will go in their countersunk holes in the intake just before we reinstall the fuel rail and injectors.
    Wrap the rail in a clean cloth and set aside. Note that you MUST install the injectors to the rail FIRST. If you try to put the injectors into the manifold then install the rail on top of them, you will destroy the O-rings.
  12. Remove the six bolts from the EGR chamber plate. They have been sealed with silicone so they may be tight. Use a sudden quick rap on the ratchet handle to break them loose. Remember we are dealing with steel bolts in an aluminum intake and threads can be stripped easily.
  13. Remove the EGR Chamber Plate and its gasket. Smooth the surface of the intake where the plate seals to remove dirt or corrosion. I used a nylon pot scrubber. NO metal or sandpaper please. Flip the plate over and examine it (see photo above). It looks like a maze with one big hole and fat runner where the exhaust comes into an "antechamber" before it flows out into smaller runners that lead to four small round dead ends. These fit over the four small holes in the gasket (see photo above) and into four holes in the intake (see photo above) and thus into the engine.
    Clean all the carbon out of the runners and dead ends with a small screwdriver, Dremel tool and brush, or whatever you can come up with.
  14. Using a drill bit with a hex shank or wad of tape (to prevent accidentally dropping the bit into the intake - very bad!) twist the bit in the four intake manifold holes that sit under the dead ends of the EGR Chamber Plate in the normal rotation so the carbon comes up out of the hole and can be vacuumed up. I started with a small drill and gradually increased the diameter until I was out to the metal. Do not cut any metal as it will get into the engine and cause damage. Just the carbon. Nothing but the carbon. Vacuum up well.
  15. Place the EGR Chamber Plate gasket in place (only fits properly one way) and then the EGR Chamber Plate. Coat the threads of the six bolts with Honda silicone sealant and start all the bolts into their threads by hand. Snug them up gently in a cross pattern and then a final tightening. Don't have a torque spec on them but I guess it is about 8 ft. lbs. Hold the ratchet close to the head to do the final tightening. Don't overtighten!!. I think the holes for these bolts go all the way through, thus the Honda sealant. The bolts had some residue on them that had to be leftover from the factory cause these bolts have never been out.
    If you decided to replace the EGR valve itself, this is a good time to do it. No instructions necessary for that. Except that if you don't have a wobble extension, the nuts are hard to get off. A wrench would probably do it if the injector rail is out of the way, so if you are going to do it, do it now.
    Wobble extensions (see a diagram of one) are just normal socket extensions except the ends are not straight but rather have a curve to each of the 4 faces that contact the drive hole in the socket and allow a gentle cant of the socket. Use of more than one gives even more ability to gently curve around obstacles. The EGR valve hangs out a little over the studs that hold it in place so the wobbles allow you to still get a good purchase on the stud nut. A true universal joint would be too big. You need to use a small 6 or 12 pt socket and wobble extensions to get it.
  16. Remove the paper towels wads from the injector holes. Clean out any crud from the recessed hole where the seal ring for the injector goes. Coat the new seal ring with engine oil (do NOT use ANY other substance!) and install. The seal ring is reversible; there is no up and down.
  17. Put the fuel rail banjo bolt hose back thru from whence it came and gently fit the tip of the injectors into the seal ring holes. Go slowly 'cause they fit tightly. A bit of engine oil on the injectors and the seals  helps. Wiggle and push. Some force is needed. Keep pushing until they seat fully, and watch for binding. Start the nuts on the studs that hold the rail down. Tighten them slowly a little at a time alternating between the two studs until everything is snugged up (7 ft/lbs ONLY). Put all the vacuum and other rubber hoses (especially the fuel return line!!) back on. Install the wiring cover after you hook up the EVAP purge control valve solenoid wires and hoses. Reconnect all the injector electrical connectors.
  18. Put a new washer on the fuel filter banjo bolt, then banjo bolt through the banjo fitting, then another washer on the other side of the fitting, then thread it into the fuel filter. Hold the wrench on the hex below the banjo bolt and holding that wrench steady,  tighten the banjo bolt. This bolt is hollow so don't overtorque it. Book says 25  ft lb if you have a torque wrench.
  19. Inspect your work. Make sure all hoses are back on. Tighten gas cap. Reconnect the negative terminal on battery. Cycle ignition key on/off (leave it at "II" until the Check Engine light goes off; two seconds) so that the pump runs but starter does NOT engage. Do this three times inspecting for leaks after each cycle. If you don't see any leaks, clean up your tools and start the car. You should let it run for a good while after the fans cycle to let it reprogram its base idle.
  20. Total work time is roughly two hours, give or take.

Last updated: May 20/08