In late 2008, Yamaha announced they would release an all new R1 for 2009. The new R1 takes engine technology from the M1 MotoGP bike with its cross plane crankshaft. Crossplane technology puts each connecting rod 90° from the next, with an uneven firing interval of 270°- 180°- 90°- 180°. The 2009 R1 was the first production sportbike to use a crossplane crankshaft and big-bang firing order. The power delivery is the same as a 90° V4 with a 180° crank, such as the Honda VFR800 and very similar to the Yamaha V-Max which has been lauded for its exhaust sound. Yamaha claims the bike would give the rider ‘two engines in one’, the low end torque of a twin and the pace of an inline four. As with previous incarnations of the R1, the 2009 model keeps its Yamaha Chip Controlled Throttle (YCC-T).
Another advancement included on the 2009 model was D-Mode Throttle Control Valve Mapping, which allows a rider to choose between three distinct maps depending on the rider’s environment. Each mode of operation controls YCC-T characteristics, changing how the R1 reacts to rider input. The first mode is Standard Mode, which delivers performance for a wide variety of driving conditions. The second mode is “A” mode which will give a rider more available power in the lower to mid RPM range. The third mode is “B” mode, which is a dial back of the previous mode, designed to soften throttle response in inclement weather and heavy traffic. D-Mode throttle control is controlled by the rider through a forward mode button near the throttle. The instrument panel is more comprehensive than previous models, and the 2009/2010 Yamaha YZF-R1 model had a gear indicator as standard.
Overall handling of the R1 was improved through changes to frame and suspension. A new sub frame was designed for the 2009 R1, cast from magnesium giving lower weight aiding mass centralisation. The rear shock absorber on the 2009 offers variable speed damping, as well as an easy to tweak pre-load via a screw adjustment. The rear shock now connects underneath the swing arm through a different linkage; a change from previous years’ models. To improve overall handling and safety, Yamaha included an electronic steering damper.
The front has the same classic R1 shape, though the air intake location and headlamp design have been revamped on the 2009 model; using only projector lamps, and using the new-found design space within the nose cone to reroute ram air tubes next to the lights.
Testing the 2010 model year in the confines of a tri-oval racetrack, Motorcyclist magazine reported a 1⁄4-mile (400 m) time of 10.02 seconds @ 144.23 mph (232.12 km/h), and fuel consumption of 25 miles per US gallon (9.4 L/100 km; 30 mpg‑imp). Motorcycle Consumer Newsreported a tested top speed of 176.7 mph (284.4 km/h).
In 2011, the R1 received a new front design and other minor changes.
In 2012 the Yamaha YZF-R1 received traction control and a special edition 50th Anniversary R1 was released. The special edition color is inspired from Assen TT-winning MotoGP bike. The special edition commemorates the participation of Yamaha in MotoGP.