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.
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".
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 to , while the total fuel tank capacity was unchanged at . 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.