1998–1999
Yamaha launched the YZF-R1 after redesigning the Genesis engine to offset the crankshaft, gearbox input and output shafts. This "compacting" of the engine yielded a huge dividend in that the total engine length was now much shorter. This allowed the wheelbase to be shortened significantly which resulted in much quicker handling and an optimized center of gravity. The bike had a compression ratio of 11.8:1. with a 6-speed multi-plate clutch transmission.
The launch model Yamaha YZF-R1 was available in white/red or blue. Early models were subject to a worldwide recall for a clutch problem. Yamaha today describes the launch of the R1 as the true value of "Kando"
Motorcycle Consumer News tests of the 1998 model year YZF-R1 yielded a 0 to 60 mph (0 to 97 km/h) time of 2.96 seconds and 0 to 100 mph (0 to 160 km/h) of 5.93 seconds, a ¼ mile time of 10.19 seconds at 131.40 mph (211.47 km/h), and a top speed of 168 mph (270 km/h), with deceleration from 60 to 0 mph (97 to 0 km/h) of 113.9 ft (34.7 m). For the 1999 model year, Cycle World tests found a 0 to 60 mph (0 to 97 km/h) time of 3.0 seconds, ¼ mile time of 10.31 seconds at 139.55 mph (224.58 km/h), and a top speed of 170 mph (270 km/h).

2001 YZF-R1
2000–2001
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 414 lb (188 kg) dry. At 127.8 bhp (95.3 kW) at the rear wheel, 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. Also updated is the seating area. The fuel tank is reshaped with a more relaxed rear angle and deeper leg recesses to provide for better rider feel. The seat extends further towards the front of the tank and the new, steeper seating position puts additional weight on the front end. All of this is aimed at improving weight bias and offering sharper cornering and more stability. Again, the resounding theme here is to sharpen what was already a very sharp package. The carburetors have been rejetted in an effort to improve throttle response—especially in the low end—all the way up to the bike's 11,750 rpm redline. The redesigned camshafts are lighter and use internal oil ways to lubricate journals that, when combined with reduced tappet clearance, provide less friction and create less engine noise. Also changed within the crankcase is the gearbox featuring a taller first gear, a hollow chrome-moly shift-shaft with an additional bearing and a completely redesigned shift linkage and foot pedal. These changes are aimed at nixing last year's transmission complaints as well as helping to transfer as seamlessly as possible the R1's prodigious power to the pavement.2002–2003

2002 YZF-R1 with aftermarket high-mount exhaust
In 2002, Cycle World reported fuel mileage of 38 mpg-US (6.2 L/100 km; 46 mpg-imp), a 0 to 60 mph (0 to 97 km/h) time of 2.9 seconds, a ¼ mile time of 10.32 seconds at 137.60 mph (221.45 km/h), and a top speed of 167 mph (269 km/h).
2004–2005

2004 YZF-R1

2006 YZF-R1
2006
The 06 R1 produces 132-134 horsepower at the rear wheel In addition, the swingarm was extended 20 mm longer due to acceleration instability. Also, in 2006 the 50th anniversary of Yamaha racing in America, Yamaha released the limited edition version in original Yamaha racing colors. The model (LE/SP) featured a Kenny Roberts replica paint pattern with yellow and black paint, and 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 shaved nearly a pound of unsprung weight. And a back torque-limiting slipper clutch, and an integrated lap timer rounded out the package making the LE more of a production racer. It had an MSRP of $17,999 and only 500 units were made for the United States.
2007–2008

2007 Yamaha YZF-R1 used by Noriyuki Haga in the Superbike World Championship.