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Yamaha R1 3rd Gen (2004-2006) Maintenance Schedule and Service Intervals

2006 Yamaha YZF-R1

This is the maintenance schedule and associated service intervals for the 2004-2006 Yamaha R1, the third generation of R1.

The third generation Yamaha R1 added ram air and braking improvements to the second generation R1. It also included the stunning 2006 50th Anniversary Edition Yamaha R1, one of the most gorgeous models released ever, and perhaps more street-worthy than the 2016 60th Anniversary Edition Yamaha R1, which came later.

Yamaha introduced ride by wire in the 4th generation 2007-2008 R1.

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What you need to service the 2004-2006 Yamaha R1

Below is a list of consumable items you may need to service your 2004-2006 Yamaha R1.

Part/consumableImage2004-2006 Yamaha R1 3rd Gen specification.
Engine oil Yamalube yamaha engine oil Yamaha recommends using their own motor oil, which is affordable and good. Yamalube 10W-50 covers a huge range of operating temperatures, from below freezing to above 100 degrees F / 40 degrees C. Or use a high-grade synthetic like Motul 7100.
Oil filter K&N oil filter Replace every 2nd oil change. Many 3rd gen R1 owners use Hiflofiltro filter HF303RC for easy replacement (you can use a normal wrench).
Spark plugs NGK spark plugs You need four spark plugs for the YZF-R1, NGK CR9EK for the 2004-2006 Yamaha R1.
Air filter air filter generic pic Use K&N air filter YA-1004 for the 04-06 model.
Chain lubricant motorcycle maintenance tools - motul chain paste A really popular chain lubricant that’s low-mess and highly effective is Motul chain paste.
Coolant Zerex valvoline coolant Valvoline Zerex G05 meet’s Yamaha’s requirements for an ethylene-glycol anti-freeze with corrosion-prevention properties.
Cable lubricant motorcycle maintenance - cable lubricant Keeping good clutch action depends on having a well-lubricated chain. You can use engine oil, but Protect All Cable Life is an affordable and well-used staple of maintenance.
Mechanical grease It’s important to grease moving parts, like the sidestand and sometimes bearings, to keep them from getting notchy or seizing. Valvoline moly-fortified grease meets a lot of needs.
2004-2006 3rd Gen Yamaha R1 consumables

2004-2006 Yamaha R1 (3rd Gen) Maintenance Schedule

Below is the maintenance schedule for the 2004-2006 Yamaha R1 third generation.

Maintenance notes:

  1. Yamaha recommends that you get a dealer or mechanic to service everything other than the brakes, chain, and lubricating the controls.
  2. The maintenance schedule includes miles from the US manuals, and KM from the European ones. They don’t match up exactly, but are similar in order of magnitude.
  3. After the last maintenance interval, continue repeating every second column.
  4. Maintaining the chain: Check, clean, and lube the chain every 500 mi (800 km) and after washing the motorcycle or riding in the rain
  5. Maintaining the air filter:
    1. This model’s air filter is equipped with a disposable oil-coated paper element, which must not be cleaned with compressed air to avoid damaging it
    2. The air filter element needs to be replaced more frequently when riding in unusually wet or dry areas
  6. Maintaining the hydraulic brakes
    1. After disassembling the brake master cylinder and calipers, always change the fluid.
    2. Regularly check the brake fluid levels and fill the reservoirs as required
    3. Every two years replace the internal components of the brake master cylinder and calliper, and change the brake fluid
    4. Every four years (or if cracked or damaged) replace the brake hose.

The maintenance for the 2006 Yamaha YZF-R1 is broken into two sections: periodic maintenance for emission control systems, and general maintenance and lubrication.

Periodic Maintenance Emission Control System

mi x 1000 (US)48121620
km x 1000 (Europe/APAC/NZ)10203040
Fuel line• Check fuel hoses for cracks or damage
• Replace if necessary
Spark plugs• Check condition
• Adjust gap and clean
• Replace periodically (R) with NGK CR9EK
Valve clearance• Check and adjust valve clearance (every 26.6K mi, 42K km)
Crankcase breather system• Check breather hose for cracks or damage
• Replace if necessary
Fuel injection• Check and adjust engine idle speed and synchronization
Exhaust system• Check for leakage
• Tighten if necessary
• Replace gasket(s) if necessary
Evaporative emission control system (For California only)• Check control system for damage
• Replace if necessary
Air induction system• Check the air cut valve and reed valve, and hose for damage
• Replace any damaged parts if necessary
Emissions maintenance for the 3rd gen Yamaha R1 – 2004-2006

General Maintenance and Lubrication Chart

Distance (mi, US)48121620
Distance (km, Eur/Aus)10203040
Time (mon)612182430
Air filter element• Check condition and damage.
• Replace if necessary (K&N YA-1004)
Clutch• Check operation.
• Adjust or replace cable.
Front brake• Check operation, fluid level, and for fluid leakage.
• Replace brake pads if necessary.
Rear brake• Check operation, fluid level, and for fluid leakage.
• Replace brake pads if necessary.
Brake hoses• Check for cracks or damage.
• Replace (Every 4 years)
Wheels• Check runout and for damage.
• Replace if necessary.
Tires• Check tread depth and for damage.
• Replace if necessary.
• Check air pressure.
• Correct if necessary.
Wheel bearings• Check bearings for smooth operation.
• Replace if necessary.
Swingarm pivot beraings• Check bearing assemblies for looseness.
• Moderately repack (R) with lithium-soap-based grease.
Drive chain• Check chain slack/alignment and condition
• Adjust and lubricate chain (Motul chain paste)
Steering bearings• Check bearing assemblies for
• Moderately repack (R) with lithium-soap-based grease every 16000 mi (25000 km) or 24 months.
Steering damper• Check operation and for oil leakage
Chassis fasteners• Check all chassis fitting and fasteners.
• Correct if necessary.
Brake and clutch lever pivot shafts• Apply lithium-soap-based grease lightly.
Sidestand pivot• Check operation.
• Apply lithium-soap-based grease lightly.
Sidestand switch• Check operation and replace if necessary.
Front fork• Check operation and for oil leakage.
• Replace if necessary.
Shock absorber assembly• Check operation and for oil leakage.
• Replace if necessary.
Rear suspension link pivots• Check operation.
• Correct if necessary.
Engine oil• Change (warm engine before draining) (Motul 7100)
Engine oil filter cartridge• Replace (HF303RC)
Cooling system• Check hoses for cracks or damage.
• Replace if necessary.
• Change (Zerex G05)
EXUP system• Check operation, cable free play and pulley position (every 12K mi/30k km)
Front and rear brake switches• Check operation
Control cables• Apply lubricant thoroughly (Protect all cable life)
Throttle grip housing and cable• Check operation and free play.
• Adjust the throttle cable free play if necessary.
• Lubricate the throttle grip housing and cable.
Lights, signals and switches• Check operation
• Adjust headlight beam
Maintenance schedule for the 3rd gen Yamaha R1 – 2004-2006

About the 2004-2006 3rd Gen Yamaha R1

The 2004-2006 Yamaha R1 brought with it ram air and some brake improvements (that mean that the brake part numbers are different to earlier models)

Ram air means that at higher speeds, air is forced into the inbox, forcing more fuel/air mixture — like a turbocharger. It works, with claimed power at speed being a few kW more than at standstill.

The 2004-2006 Yamaha R1 also has a longer swingarm to increase stability.

In 2006, Yamaha also released the drop-dead-gorgeous anniverary-edition Yamaha R1, which is already a collector’s item (good luck finding one).

Yamaha also released the SP with this generation, with a custom Öhlins suspension and forged marchesini wheels, much like the S-series Ducati super bikes of the time.

Finally, there was the LE, produced in a limited run of 500 — but we’re not talking about those right now.

Manual for the 2004-2006 Yamaha R1 3rd Gen

2006 Yamaha YZF-R1 Maintenance schedule screenshot from manual

The above information was gleaned from the owner’s manual for the 2006 Yamaha YZF-R1.

You can download it from Yamaha’s website here.

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