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.

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).

The Yamaha R1 1999 Model