The YZR-M1 — the name standing for "Mission One" — debuted in the 2002 season, the first year that 990cc four-stroke machines were permitted alongside the outgoing 500cc two-strokes. Departing from the V4 layout of its predecessor, Yamaha chose an inline-four engine configuration, which engineers believed offered the best balance between the motor and chassis. The original design retained five valves per cylinder and began the season with a 942cc displacement before reaching the full 990cc limit mid-season. Carburetion gave way to fuel injection for 2003, and the bike used an engine braking control system later replaced by an Idle Control System to improve stability under deceleration.
Max Biaggi, Carlos Checa, and other riders campaigned the early M1 with modest results. Biaggi took two victories in 2002 and finished second in the standings, but the machine could not yet match Honda's RC211V.
The turning point came when Valentino Rossi signed a two-year contract with Yamaha for 2004, bringing crew chief Jeremy Burgess and most of his technical team from Honda. Over the winter of 2003–2004, engineers under project leader Koichi Tsuji switched the cylinder head from a five-valve to a four-valve configuration and changed the engine's firing order from the standard "screamer" layout — with equal 180-degree intervals — to a "long-bang" sequence spaced 270°-180°-90°-180°. This arrangement was designed to replicate the constant kinetic energy delivery of a V4 while retaining the compact packaging of an inline-four, and it transformed the bike's traction characteristics at corner exits.
The revised M1 set the fastest lap in pre-season IRTA testing at Catalunya and went on to win the opening race of 2004 at Welkom, making Rossi the first rider to win consecutive Grands Prix on different manufacturers. He collected nine victories that season, securing the Riders' Championship, with Honda's Sete Gibernau finishing second. Rossi and the M1 repeated as champions in 2005 with a dominant margin of 147 points, a season Rossi would later describe as the greatest bike he had ever ridden.
The 2006 campaign brought chassis chatter problems caused by the simultaneous introduction of higher engine power, a stiffer frame, and a revised Michelin tyre compound. The issues were largely resolved by mid-season, and Rossi came within five points of champion Nicky Hayden at the final round — despite Rossi winning five races to Hayden's two.
Regulations reduced the premier class displacement to 800cc for 2007. The smaller-engined M1 proved faster than its 990cc predecessor straight out of pre-season testing, benefiting from later braking points, higher corner speeds, and more manageable traction. The sponsor livery also changed, transitioning from Camel to Fiat. Casey Stoner took the 2007 title for Ducati, but Rossi won the 2008 championship by a record margin. That same season, Jorge Lorenzo claimed his first premier-class win at the Portuguese Grand Prix as a rookie. Rossi and Lorenzo combined to win ten races in both 2008 and 2009, with Rossi securing his seventh and final MotoGP title in 2009. Lorenzo won the championship in 2010, giving Yamaha back-to-back constructors' titles.
For 2012, regulations raised the maximum displacement to 1000cc with a four-cylinder limit and a maximum bore of 81mm. Jorge Lorenzo claimed that year's Riders' Championship closely followed by Honda's Dani Pedrosa. The M1 continued as a frontrunning machine through subsequent seasons, with Lorenzo winning again in 2015 and Fabio Quartararo claiming Yamaha's most recent title in 2021.
In 2025, after more than two decades relying on the crossplane inline-four, Yamaha unveiled a V4-powered prototype version of the M1 ahead of the San Marino Grand Prix at Misano. Test rider Augusto Fernandez debuted the new configuration as a wildcard entry, gathering data rather than chasing results. The accompanying aerodynamic package featured revised tail design, repositioned gill-shaped vents, side wings, and a redesigned exhaust system with two mufflers. The move was framed as preparation for the 2026 season, though the new engine would have limited competitive life before the 2027 regulations reduce displacement to 850cc.
Through 2025, the YZR-M1 has achieved eight Riders' World Championships (Rossi in 2004, 2005, 2008, 2009; Lorenzo in 2010, 2012, 2015; Quartararo in 2021), five Constructors' titles (2005, 2008, 2009, 2010, 2015), seven Teams' championships, 125 race victories, and 126 pole positions.