Yamaha launched the YZF-R1 after redesigning the Genesis engine to offset the crankshaft, gearbox input, and output shafts. This "compacting" of the engine made the total engine length much shorter. This allowed the wheelbase to be shortened significantly, resulting in much quicker handling and an optimized center of gravity. The bike had a compression ratio of 11.8:1 with a six-speed transmission and multi-plate clutch.
The 1999 R1 saw only minor changes, apart from paint and graphics. Notable improvements were a redesigned gear change linkage and the gear change shaft length being increased. Fuel tank reserve capacity was reduced from 5.5 to 4.0 litres (1.2 to 0.9 imp gal or 1.5 to 1.1 US gal), while the total fuel tank capacity was unchanged at 18 l (4.0 imp gal; 4.8 US gal). A second worldwide recall was issued for 1998 and early 1999 models, to change a coolant hose clamp under the fuel tank which could come loose under hard use.
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 1⁄4-mile (400 m) 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 time of 3.0 seconds, 1⁄4-mile time of 10.31 seconds at 139.55 mph (224.58 km/h), and a top speed of 170 mph (270 km/h).