Yamaha launched the YZF-R1 after redesigning the Genesis engine to offset the crankshaft, gearbox input and output shafts and this "compacting" of the engine yielded a huge dividend in that the total engine length was now very short. This allowed the wheelbase to be shortened significantly which resulted in much quicker handling and an optimized center of gravity.

In 2000, Yamaha introduced a series of changes to improve the bike, plus minor changes to the body work to allow for better long duration ride handling. The R1 was an excellent bike to live with on short runs, but due to its quick handling was not a favorite longer run bike. Yamaha's main design goal was to sharpen the pre-existing bike and not redesign it. Even so they instituted over 150 changes in hopes of making an already light, sleek and mean motorcycle even lighter, sleeker and meaner. For example, even with the addition of the new Air Induction System, which weighs four pounds, the overall weight of the bike is down five pounds to a claimed 385 pounds dry. At a claimed 150 horsepower at the crank, top-end output remains the same but changes to the engine management system are supposed to result in a smoother, broader distribution of power.The bodywork is still unmistakably R1 although a few changes were made resulting in a 3% reduction in the drag coefficient. The headlight housing has a sharper profile, the side panels are more aerodynamic and slippery and the windscreen has been reshaped for better rider protection. In fact the bodywork changed so much that bodywork from previous R1s will not fit the Y2K edition.

With the competition advancing, Yamaha took to a major development. This included style updates like an underseat exhaust, and performance upgrades including radial brakes and for the first time on an R1 Ram-air intake. Furthermore, the wheelie-tendency known from earlier productions is drastically reduced by changing frame geometry and weight properties. The all new engine (no longer used as a stressed member of the chassis) featured a separate top crankcase and cylinder block. The 2004 R1 produces a stated 172 hp at the crankshaft (excluding RamAir) and also weighs 172 kilograms. Also newly added for this year was a factory installed steering damper.

In 06, Yamaha is now mated with 180 hp at the flywheel. In addition, due to acceleration instability, the swingarm was extended 20 mm longer. Also, in 2006 the 50th anniversary of Yamaha racing in America, Yamaha released a Limited Edition yellow/white/black bike in original Yamaha racing colors. They also made a limited edition model (LE/SP) featuring a Kenny Roberts replica paint pattern with yellow and black paint, front and rear custom Öhlins suspension units developed by the people who work on the YZR-M1 MotoGP bike. Custom forged aluminum Marchesini wheels specifically designed for the LE remove nearly a pound of unsprung weight. A back torque-limiting slipper clutch, , Brembo brakes, and an integrated lap timer switch on the right handle bar round out the package making the LE more of a production racer. It has an MSRP of $17,999 and only 500 units were made for the United States.

An all-new YZF-R1 for the 2007 model year was announced on 9 October, 2006. Key features include an all-new inline four-cylinder engine; going back to a more conventional 4-valve per cylinder rather than Yamaha's trade mark 5-valve genesis layout. Other new features are the Yamaha Chip Control Intake (YCC-I) electronic variable-length intake funnel system, Yamaha Chip Control Throttle (YCC-T) fly-by-wire throttle system, slipper-type clutch, all-new aluminum Deltabox frame and swingarm, six-piston radial-mount front brake calipers with 310 mm discs, a wider radiator, and M1 styling on the new large ram-air ports in the front fairing. 2008 brought BNG and the ability to buy limited edition Fiat plastics.