The 2006 MotoGP season was one of the closest battles in recent years, in which Honda's Nicky Hayden did not claim the championship from Valentino Rossi until the final race of the year. The victory was Hayden's first and only World Championship. Seven different riders claimed Grand Prix victories including first time winners Dani Pedrosa, Toni Elías and Troy Bayliss. Yamaha's Valentino Rossi fought back from a 51-point deficit to lead the championship going into the final rounds. Hayden's fortunes took a dip when he was taken out by his teammate Pedrosa at the penultimate round in Portugal, but he bounced back to win the crown when Rossi crashed in the final race at Valencia. Hayden only won two races to Rossi's five, but the Yamaha suffered a number of mechanical issues which led to more retirements which allowed Hayden to score more podiums. Also, the surprise win of Elias in Portugal, with a margin of just 0.002 second over Rossi, proved to be a major decider in the championship. Rossi had given up five points in that round, the same amount by which he was behind Hayden in the final standings. Had there been a tie, Rossi would have been crowned World Champion due to more race victories than Hayden.
The rule regarding the interruption of a race via a red flag has been reformed. From the moment the red flag is shown, riders who are not competing actively in the race will not be classified. Once five minutes have passed since the showing of the red flag, all riders who have not reached the pits on board their motorcycles will not be classified.
Rules for licenses have been updated. All Chief Medial Officers (CMO) and Deputy Chief Medical Officers must now be in posession of a license. The license will be valid for a span of three years and be handed out by the FIM.
Criteria and procedure for the obtainment of a CMO license has been updates. Potential candidates should apply via a letter through their FMN to the FIM including their professional and motorsport CV, as well as evidence that the following criteria has been fulfilled:
- Be a fully registered and qualified medical practicioner.
- Be experienced in the supply of Emergency Medical Care.
- Be experienced at motorcycle events and must have been to at least five national events as CMO or Deputy CMO with a confirmation by their FMN.
- Have attended and successfully completed a FIM CMO seminar and have taken part in at least one FIM event within the previous two years.
In the 125cc and 250cc classes, rookie riders will now be allowed to compete in other held at circuit in Europe during a season.
These rules were additionally added on the 27th of June 2006:
Practice restrictions have been put in place for the 125cc and 250cc classes. Contracted teams who profit from a Participation Agreement to participate in the 125cc and 250cc class championships are forbidden to practice with their bikes at any circuit between the 1st of December of one year and the 20th of January of the next year, both dates being inclusive.
A change has been made regarding fuel tank regulations. In all classes, fuel tanks made out of non-metallic composite materials must be fitted with a fuel cell bladder or have otherwise passed the appropriate FIM test standards.