In 2000 Yamaha launched a series of changes to the bike, as Yamaha’s goal was to give the bike a sleeker look to the existing bike and not to redesign it. The newer version had a new air induction system. New body designs were given to the bike. The headlights had a sharper shape; the panels of the bike were made more aerodynamic to handle the air friction better.

Later on in 2003 to 2010, fuel injection system was introduced in the bike, whereas the engine size during the 2002 to the 2003 era remained the same. But In 2009 -10 Yamaha took in a major development during the years, which included many style updates like an under seat exhaust system was introduced, performance updates with radial bikes and a ram air intake.

A separate and a new cross plane crank shaft and a cylinder block was installed for the new engine, which produced an output of 132 to 134 horse power. Another advancement in the D-mode throttle control mapping model, which gave the rider an option to choose from 3 different maps depending on the environment. A new sub frame was designed for the R 1model, which is magnesium cast in carbon fiber mold, which was lighter and helped the biker to reach up high top speeds.