Born in Cerro Veronese, Veneto, Cunego began cycling as a teenager after being a successful cross-country runner. He was discovered by Giuseppe Martinelli who also worked closely with Marco Pantani. Cunego turned professional in 2002 at the age of 20 with, winning the Giro d'Oro and the Giro Medio Brenta in his first season. In 2003 he won the seventh stage and the overall classification of the Tour of Qinghai Lake. He came to prominence in May 2004, winning the Giro d'Italia at the age of 22 with. Cunego's strength came as a blow to his captain Gilberto Simoni; relations between the two during the race were strained when Cunego sprinted away from Simoni to win the 18th stage after Simoni's solo breakaway. La Gazzetta dello Sport reported that as Simoni passed by Cunego, who was surrounded by journalists, Simoni pointed his finger at Cunego and angrily said "You're a bastard...you are really stupid." During 2004 he won the Giro di Lombardia in October, his 13th victory of the season. He finished the season number one in the UCI Road World Cup, the youngest rider to achieve it, aged 23. He was also the last rider ranked first on the world ranking, because from 2005 the ranking was replaced by the UCI ProTour.
Lampre (2005–14)
In the 2005 Giro d'Italia, Simoni and Cunego were co-captains of, but Cunego posed no threat to Simoni, as he faltered during the first climb in the Dolomites, losing six minutes in the day and any prospect of winning. At the time his team attributed his loss to a "psychological crisis" and Cunego said "a great weight has been lifted from me by this defeat." After the race, he was found to have Epstein–Barr virus, and he did not enter the 2005 Tour de France. In 2006, Cunego finished third in Liège–Bastogne–Liège losing to Alejandro Valverde and Paolo Bettini in a sprint finish. In the Tour de France Cunego was the winner of the young rider classification; he finished 2nd on stage 15 to Alpe d'Huez, after losing to Fränk Schleck, who broke away in the final. He also finished 3rd on stage 17, on the road to Morzine. In 2007 Cunego again won the Giro del Trentino and his second Giro di Lombardia. In 2008 he won the Klasika Primavera and the Amstel Gold Race, with two powerful sprints against Valverde and Schleck, with victory in the latter propelling him to the top of the UCI Pro Tour rankings, as he also went on to finish second in the UCI Road World Championships. He was widely tipped to be victorious in the Tour de France, but he struggled and eventually dropped out before the finish. By the end of the year Cunego conquered for the third time at the Giro di Lombardia and then he ended the season with victory in the Japan Cup, confirming himself as one of the best Classics specialists in the world. In 2009 he won the Settimana Internazionale di Coppi e Bartali with victories in two stages; later he won two mountain stages at Vuelta a España, which made him one of the favourites for the road race at the UCI Road World Championships. He ultimately finished that race in eighth position. In July 2013, he was one of 27 former riders and officials linked to the team indicted for doping in an Italian court, with a hearing set for 10 December 2013. In early 2014 however, details emerged that indicated that Cunego might have been one of few Lampre riders to refuse treatment by Spanish doctor José Ibarguren Taus, who was linked to doping practices.