Defending champion Eddie Lawson stunned most observers by switching from the Yamaha to Honda in the offseason then proceeded to win the championship, becoming the first man to win two consecutive 500cc championships on two different brands. On why he left Yamaha for Honda: "Giacomo Agostini, the Marlboro Yamaha team manager, started playing games, saying stuff like, 'I don't know if we can pay you the same as we did in 1988.' I'd just won my third title, so that was tough to hear. Also, I found out Ago was talking to Kevin Schwantz. I met with Erv and told him that I needed a change. When Marlboro discovered I was talking with Honda, they doubled their offer, but it was too late. I actually took a pay cut to ride the Honda."
Wayne Rainey and Kevin Schwantz continued to perform impressively while Freddie Spencer made a less than successful comeback attempt with the Marlboro Yamaha team. Australian Wayne Gardner was out for most of the season after breaking his leg at Laguna Seca but not before winning the inaugural Grand Prix in his home country. Another Australian made his Grand Prix debut for the Rothmans Honda team with Mick Doohan scoring a third place finish at the Hockenheimring. The FIM awarded half points for the rain-drenched Belgian Grand Prix after organisers restarted the race three times contrary to FIM race regulations. The Nations Grand Prix at Misano was boycotted by most of the top riders for safety reasons.
Sito Pons won a second consecutive 250 championship for Honda while Spanish teenager, Àlex Crivillé won the 125 crown on a JJ Cobas. Derbi rider Manuel Herreros had the honor of winning the final 80cc championship as the class would be discontinued after 1989.