Your check engine light just flashed on, and your scanner shows P1399. Before you panic or dump money into random parts, let’s clear up what’s actually going on with your Honda. This code doesn’t mean your car’s about to explode—but it does need attention. Here’s everything you need to know to fix it right the first time.
What Is the Honda P1399 Code?
P1399 is Honda’s way of telling you there’s a random cylinder misfire happening. Unlike codes P0301 through P0306 that point to a specific cylinder, P1399 means the problem’s bouncing around or affecting multiple cylinders at once.
Here’s the catch: many generic scan tools will tell you P1399 is a “Glow Plug Circuit” fault. That’s completely wrong for Honda’s gasoline engines—it’s just using a definition from diesel vehicles. Ignore that misleading label.
Your Honda’s computer monitors how fast the crankshaft spins after each combustion event. When a cylinder doesn’t fire correctly, the crank slows down for a split second. If this happens often enough, P1399 gets logged.
The Real Culprits Behind P1399
Tight Valves: The Silent Killer
If you’re driving an older Honda or Acura with high mileage, tight valves are your most likely suspect. Honda engines use mechanical valve adjusters that need periodic tweaking—not the self-adjusting hydraulic lifters many other brands use.
Over time, your valve seats wear down from millions of combustion cycles. This pushes the valve stems higher, reducing the clearance (or “lash”) between the valve tip and rocker arm. Eventually, there’s zero gap left.
When that happens, your valves can’t fully close. They stay slightly open, which kills compression and prevents proper cooling. The valve can’t shed heat without touching its seat, leading to a burnt valve and a severely damaged head.
Factory valve clearances:
- Intake: 0.008-0.009 inches
- Exhaust: 0.011-0.013 inches
When clearance drops to zero, you’ll get rough idle, misfires that trigger P1399, and eventually permanent engine damage. A valve adjustment typically costs $400-$800 and should be done every 50,000-100,000 miles.
Clogged EGR Passages: The V6 Nightmare
Honda V6 engines—especially in Odysseys, Pilots, and Accords—have a nasty habit of clogging their EGR distribution ports. The exhaust gas recirculation system reduces emissions by routing some exhaust back into the intake.
The problem? Oil vapors from your PCV system mix with carbon-rich exhaust, creating a thick sludge that hardens in the narrow distribution ports. When some ports clog while others stay open, you get uneven distribution.
Cylinders with open ports get flooded with exhaust gas—which doesn’t burn. The air-fuel mixture gets so diluted that combustion either weakens dramatically or fails completely. Your computer detects the misfire and logs P1399.
The telltale sign: the misfire disappears at idle and wide-open throttle (when EGR is closed) but shows up during steady highway cruising. Cleaning requires removing the intake plenum and physically scraping the carbon out.
Ignition System Failures
Your ignition system can cause P1399 in sneaky ways:
Coil-on-Plug Issues
When an ignition coil starts failing, it doesn’t always die completely. A “weak” coil might work fine when cold but break down under heat or load. Even stranger, a failing coil can create electromagnetic interference that messes with neighboring coils or the crankshaft sensor itself. Your computer sees random misfires instead of pointing to one cylinder.
Distributor Problems (Older Models)
For 1997-2001 CR-Vs and similar vintage Hondas, distributor issues are common. Carbon tracking on the cap—tiny conductive lines that form on the plastic—can send spark to the wrong cylinder or straight to ground. Oil leaking through the distributor seal can contaminate internal sensors, causing timing synchronization issues that trigger P1399.
| Component | What Fails | When It Acts Up |
|---|---|---|
| Ignition Coil | Insulation breakdown | Under heavy load or high heat |
| Spark Plugs | Gap erosion, carbon buildup | Hard starting, poor fuel economy |
| Distributor Cap | Carbon tracking, moisture | Damp weather, cold starts |
| Plug Wires | Resistance increase, cracking | Visible arcing in the dark when misted |
Fuel System Complications
Injector Degradation
Fuel injectors can clog partially or develop electrical issues that make them “lazy.” A clogged injector might still spray fuel, but in large droplets instead of a fine mist. This burns inefficiently and can cause misfires.
In J-series V6 engines, the plastic spray cones on injectors have been known to crack or break completely. If several injectors are marginally degraded, you’ll see a random misfire pattern that doesn’t stick to one cylinder.
Check your Long-Term Fuel Trim (LTFT) in live data. If it’s over ±10%, your computer’s struggling to maintain the correct air-fuel ratio.
Low Fuel Pressure
A failing fuel pump or clogged filter can drop rail pressure. Under high demand—climbing hills, hard acceleration—the injectors can’t deliver enough fuel. You get momentary lean misfires that affect all cylinders randomly, making P1399 the primary code instead of a specific cylinder fault.
Real-World Cases That’ll Save You Money
The “Invincible” J-Series That Wasn’t
A 2003 Acura owner threw parts at their car for months: fuel pump, VTEC solenoid, TPS, MAF, spark plugs, coils. Nothing worked. The engine even passed a compression test with flying colors.
The actual problem? A clogged catalytic converter creating backpressure. By temporarily removing the upstream O2 sensor to create an exhaust leak, performance returned immediately. The fix was replacing the converter—not all the parts that got swapped unnecessarily.
The CR-V Timing Belt Mystery
A 1999 CR-V had P1399 that survived valve adjustment, new plugs and wires, and even an ECU swap. The breakthrough came on the fourth timing check: the belt had jumped one tooth because the tensioner bolt was slightly too long and didn’t provide proper clamping force.
That tiny timing deviation was enough to create a constant random misfire profile without setting a timing-specific code.
Understanding Misfire Severity
Not all P1399 codes are equally urgent. The OBD-II system classifies them into two types:
Type A (Flashing Check Engine Light)
Severe misfires that occur within 200 engine revolutions. These dump raw fuel into your exhaust, where it ignites against the catalytic converter’s precious metal substrate. To prevent melting the converter, your check engine light will flash once per second. The computer may even shut off the fuel injector for the offending cylinder.
Type B (Steady Light)
Less frequent misfires over a 1,000-revolution window. These won’t melt your converter immediately, but they’ll cause you to fail emissions testing and lose fuel economy. Your vehicle’s emissions can exceed federal standards by 1.5 times.
Your Honda might fluctuate between these states—steady light at idle that starts flashing during hard acceleration.
Diagnostic Steps That Actually Work
Start With the Basics
Don’t skip the obvious stuff:
- Check spark plugs for wear, gap erosion, or oil fouling
- Test battery voltage (weak batteries cause weird electrical issues)
- Inspect plug wires for cracks or visible arcing
- Verify all vacuum lines are connected and intact
The Valve Adjustment Test
If your Honda has over 100,000 miles and you can’t remember the last valve adjustment, start there. It’s maintenance, not repair—and it fixes P1399 more often than anything else.
Advanced Diagnostics
When basic fixes don’t work, you need deeper analysis:
Compression and Leak-Down Testing
A compression test gives you a snapshot of peak cylinder pressure. Honda J-series engines should show 180-195 PSI. But a leak-down test is more revealing—it tells you where the leak is. Hissing from the intake means intake valve issues; hissing from the tailpipe points to exhaust valves.
Crankshaft Sensor Analysis
Using an oscilloscope on the CKP sensor lets you see the exact millisecond a cylinder’s contribution drops. This can reveal that your “random” P1399 is actually a specific mechanical fault masquerading as random.
What It’ll Cost You
The price range for fixing P1399 varies wildly based on the actual cause:
| Issue | Typical Cost (Parts + Labor) |
|---|---|
| Valve Adjustment & EGR Cleaning | $400 – $800 |
| Timing Belt Realignment | $500 – $900 |
| Distributor Replacement | $250 – $500 |
| Spark Plugs & Coils | $300 – $600 |
| Catalytic Converter | $800 – $1,500 |
Watch out for shops that automatically bundle valve adjustments with new coils and plugs. You might not need everything they’re quoting—understanding the primary causes helps you avoid the “parts cannon” approach.
Prevent P1399 From Coming Back
Regular maintenance beats expensive repairs:
- Valve adjustments every 50,000-100,000 miles (or whenever you feel a stumble at idle)
- EGR port cleaning every 60,000 miles for V6 models
- High-quality iridium or platinum spark plugs every 60,000 miles
- Timing belt replacement every 90,000-105,000 miles (don’t forget the tensioner and water pump)
Honda engines are legendary for running well past 200,000 miles—but they’re sensitive to valve lash and EGR balance. Skip these services, and P1399 becomes your constant companion.
The Bottom Line
P1399 isn’t a mystery once you understand what triggers it. For most Hondas, the solution lives in the intersection of proper valve clearance and clean EGR flow. Start with a valve adjustment if your mileage is high. Check your EGR ports if you’ve got a V6. Verify your ignition system is solid.
Don’t let the generic “Glow Plug Circuit” definition throw you off—that’s not what’s happening in your gasoline Honda. And don’t start swapping expensive parts without understanding what’s actually failing. This code is fixable, usually without breaking the bank, as long as you tackle the right problem.
