There was much speculation during the second half of the 2003 season about Rossi's plans for the future.[citation needed] Some people suspected that he would succeed in his bid to claim a third consecutive title and wondered where he would go in the future. His contract with Honda was up at the end of the year and there were rumors that Rossi had become somewhat disillusioned with his ride at Honda. His tenure at Honda had effectively run its course; he had provided Honda with a 500 cc World Championship as well as consecutive MotoGP World Championships.

Partnered with increased scepticism that the reason for his success was the dominance of the RC211V rather than Rossi, it was inevitable that Honda and Rossi would part. Mid-season rumors pointed towards a possible move to Ducati, which sent the Italian press into a frenzy; the concept of the great Italian on the great Italian bike seemed too good to be true. Ducati did indeed try to seduce Rossi into riding their MotoGP bike, the Desmosedici, but for numerous reasons Rossi passed the offer up. Critics say that compared to the other manufacturers, Ducati had a significant way to go before being competitive even with Rossi at the helm. This proved to be the truth with Ducati's lackluster performance in the 2004 season, which had actually been worse than their inaugural year in MotoGP in 2003.

In his 2005 autobiography, "What If I'd Never Tried It?", Rossi offers another reason for choosing Yamaha over Ducati, saying that the mindset at Ducati Corse was a little too similar to the one he was trying to escape from at Honda.

Ultimately, Rossi signed a two-year contract with rivals Yamaha reportedly worth in excess of (U.S) $12 million; a price no other manufacturer, even Honda, was willing to pay.

His fiercest critics[clarification needed] claimed that on an inferior machine (the Yamaha YZR-M1), Rossi would not be able to recreate his World Championship wins of the previous years, especially with increased development of the RC211V and the likes of Max Biaggi and Sete Gibernau on Hondas. The RC211V was a superior machine in almost every aspect although it was guaranteed that the gap would shrink with the defection of Rossi and Jeremy Burgess (chief mechanic for Rossi at Honda, whom Rossi had also convinced to join). The 2004 season would give Rossi the ability to show everyone, especially his critics, what he was made of and provide him with an opportunity to prove that it was his talent rather than his bike that won him his championships.

With the traditional first race of the season at Suzuka off the list due to safety considerations, the 2004 season started at Welkom in South Africa. Rossi won 8 more GP wins during the season, battling Sete Gibernau ferociously until Rossi eventually closed the door on Sete's hopes in the penultimate race of the season at Phillip Island. Gibernau and Rossi had become bickering enemies during the course of the season; whereas in previous seasons they had been competitive but friendly rivals, various disputes arose during 2004 which led to their falling apart. Rossi would continue to rub salt into the wound for both Gibernau and Honda by winning the ultimate race of the season at Valencia. It was a painful blow to both Gibernau and Honda; Gibernau, so close to a World Championship, and Honda, starting to become aware of what they had let go. Valentino Rossi ended up with 304 points to Gibernau's 257, with Max Biaggi 3rd with 217 points.

In 2005 Grand Prix motorcycle racing season, Rossi captured his 7th World Championship and 5th straight MotoGP Championship. He finished with a total of 367 points, an incredible 147 points ahead of 2nd place finisher Marco Melandri (220 pt), and Nicky Hayden finishing 3rd with 206 points.

The 2006 MotoGP season started off with Rossi, once again, being the favorite to take the Championship, but he had trouble in the first half of the season. Rossi finished 14th in Jerez, making a comeback after Toni Elias pushed him at the very first corner, and had a pair of DNFs in Shanghai and Le Mans due to tyre and electronic problems respectively. Nicky Hayden held the points lead throughout most of the season, but Rossi was slowly working his way up the points ladder. It wasn't until Motegi when Rossi finally grabbed 2nd in the points race behind Hayden. In the Portuguese Grand Prix, the second to last race of the season, Hayden was taken out by his teammate, Dani Pedrosa, and did not finish the race. This led to Rossi taking the points lead with only one race left in the season. Rossi crashed early in Valencia, the last race, and Hayden went on to win the 2006 MotoGP Championship. Rossi finished the season in 2nd place.

Valentino Rossi returned to MotoGP for the 2007 season riding the new Yamaha YZR-M1 800 cc. In the first race in Qatar he came second to Casey Stoner on the Ducati Desmosedici. In the second round of the season Rossi won the Race with Dani Pedrosa in second place and Colin Edwards in third giving both Yamaha riders podiums. Casey Stoner returned to winning ways in the third and fourth races of the season at the Turkish and Chinese grand prix on his Ducati, which has enjoyed a top speed advantage over the rest of the field. Another reason for Stoner's consistency during the 2007 season in comparison with Rossi's mixed results is the advantage Ducati's tyre supplier, Bridgestone, appeared to have over its rival, Michelin, who then supplied tyres for Rossi's factory Yamaha.

Rossi's 10th position at Turkey was put down to a defective tyre and while he managed to bounce back to a second place on the podium at China, a poor tyre recommendation from Michelin was blamed for his 6th place finish in the wet French grand prix at Le Mans. Bridgestone riders took all 3 places on the podium at the French tyre giant's home race, and Rossi went on the record to say that Michelin must urgently address various weaknesses. Rossi won at his home race, the Italian grand prix at Mugello, ahead of Dani Pedrosa, also Michelin-shod on his factory Honda. Championship leader Casey Stoner was beaten to the last podium place at Mugello by Brazilian veteran Alex Barros on a satellite Ducati with Bridgestone tyres.

Rossi's grip on the championship loosened slightly at Catalunya and Donington, finishing second and fourth respectively to winner Casey Stoner, however the Assen race was won by Rossi who charged through the field from 11th on the grid after a poor wet qualifying session to challenge and eventually beat Casey Stoner to the chequered flag by 1.5 seconds. At the half-way point of the 2007 season Rossi was the closest challenger to Casey Stoner's title aspirations, trailing by 21 world championship points. In the month of June, commonly called "Rossi's month" with races consisting of Mugello, Catalunya, Donington Park and Assen, both Valentino Rossi and Casey Stoner have scored 83 points each; 2 x 1st place, 1 x 2nd place and 1 x 4th place. This has been done in conditions favourable to the Italian manufacturer and in some cases left Rossi on the fourth row with a point to prove.

Sachsenring saw a disastrous performance from the Italian. After qualifying fourth on the grid, whilst Stoner took pole, Rossi had to use raceday to his advantage. Come Sunday, Rossi lined up with a fever of 102 degrees and dropped down to 8th by the end of the first lap. A pass on Randy de Puniet at the tight Omega corner saw Rossi lose the front, catch it then lose it completely and skid off into the gravel where his right hand clip on was damaged leaving him out of the race on lap 6. Luckily problems for Bridgestone in the blistering heat saw Stoner finish 5th stretching his championship lead by 11 points to 32 ahead of "The Doctor". A visit to Laguna Seca for the USGP, Rossi finished 4th place behind Stoner, Vermeulen, and Melandri respectively.

The end to the summer break in the 2007 season landed the MotoGP paddock at Brno, with various new changes to the Fiat Yamaha. Qualifying 6th for the race start on Sunday morning after struggling in free practice, Rossi spent his rear Michelin early on in the race chasing Capirossi to make it up to 5th. Eventually tyre issues got the best of the 7 times world champion and Rossi crossed the finish line in 7th, a whole 22 seconds behind 1st place man Casey Stoner. This left Rossi 60 points behind the Championship leader with only 150 points up for grabs.

Misano saw Rossi starting from 2nd on the grid behind Casey Stoner. An engine failure five laps in resulted in Rossi falling 85 points behind Stoner as he finished first.

A start from 3rd on the grid in Estoril ended in a no holds barred race with Pedrosa as they both accelerated out of the last corner sideways for Rossi to take the race win and gain 9 points in the World Championship on Stoner who finished in third.

For 2008 Rossi changed to Bridgestone tyres. The season started slowly with a fifth place finish in Qatar, but he took his first win in Shanghai, and also won the next two races. Mid-season, Stoner's Ducati seemed too strong for him, but Rossi took many second places, excluding the Dutch round at Assen, where he crashed on the first lap and finished 11th. Rossi then won at Laguna Seca after an incredible pass down the corkscrew over Stoner, who crashed but continued and took the second place. Stoner crashed out from the lead in next two races whilst under pressure from Rossi, and failed to score, while Rossi won both. After winning a rain-shortened race in Indianapolis, once again completing the achievement that he has won in every current circuit in the calendar, he needed only third place in Motegi to win. He won at Motegi too, his first win there with a four-stroke bike, clinching his first title in 800cc MotoGP, sixth in premier category, and eighth in total.

On June 8, 2009, Valentino Rossi rode a Yamaha around the famous Isle of Man TT Course in an exhibition lap along-side fellow Italian motorcycle legend Giacomo Agostini, in what was called 'The Lap of the Gods'.[9]

On June 27 2009, at the Dutch TT in Assen, he clinched his 100th victory, becoming the second rider in motorcycle grand prix history to reach 100 wins.[10]

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