With the competition advancing, Yamaha made some major changes to the model. This included style updates, like an under seat twin exhaust, and performance upgrades including radial brakes, and, for the first time an R1 Ram-air intake. Furthermore, the tendency forwheelies by earlier productions was reduced by changing the geometry of the frame and weight distribution. The all-new engine was no longer used as a stressed member of the chassis, and featured a separate top crankcase and cylinder block.
The 2004 R1 weighs 172 kilograms (380 lb) dry. The conventional front brake calipers were replaced by radially-mounted calipers, activated by a radial master cylinder. A factory-installed steering damper was also added this year. Combined with the changes to the frame, this helped to eliminate the tendency of the handlebars to shake violently during rapid acceleration or deceleration on less-than-perfect surfaces (aka "tank slapping").