The 2005 ProTour was the first year of the newly introduced UCI ProTour system, in which the ProTour teams are guaranteed, and obliged to, participate in the series of ProTour races. In certain ways the ProTour replaced the UCI Road World Cup series of one-day races, which in 2004 was won by one-day specialist Paolo Bettini for the third time in a row. The beginning of the ProTour saw difficult negotiations with the organizers of the Grand Tours, the Tour de France, the Giro d'Italia and the Vuelta a España.
Following tradition, Team CSC had a strong showing in the early season, with a commanding control of the season opener Paris–Nice, placing American Bobby Julich on the top step of the General classification, combining his strong prologue individual time trial performance and good placing in the Mont Faron queen stage. Sprinter Alessandro Petacchi shed some weight over the winter and built up a strong base to win the classic Milan–San Remo convincingly, leading to speculation that he will be the undisputed Italian team leader for the World Cycling Championship in Madrid later in the season.
The 2007 UCI ProTour is the third year of the UCI ProTour system. Following a dispute and power struggle between the UCI and the organisers of the Grand Tours, ASO, RCS and Unipublic, a number of events were run as ProTour events, although without ProTour licences. This meant the races counted towards the ProTour standings, although the organisers were not obliged to invite all 20 UCI ProTeams, notably not inviting Unibet.com.
After numerous doping scandals in previous years, culminating with Floyd Landis' doping scandal in the 2006 Tour de France, the Phonak team was disbanded when the new title sponsor, iShares, decided to cease sponsoring and pull out of cycling. As of December, 2006, the ProTour license abandoned by Phonak has been granted to the Unibet.com, and the Active Bay group of Manolo Saiz has lost its license, which was given to the Astana. The links between the ProTour and the organisers of the three Grand Tours (ASO, RCS MediaGroup and Unipublic) remain strained.
The 2008 UCI ProTour is the fourth year of the UCI ProTour system. Following protracted disagreement between the organisers of the Grand Tours (ASO, RCS and Unipublic) and the UCI, all races organized by ASO, RCS and Unipublic were withdrawn from the ProTour calendar. This removed all three Grand Tours (Giro d'Italia, Tour de France and Vuelta a España), four of the five monuments (Milan–San Remo, Paris–Roubaix, Liège–Bastogne–Liège and Giro di Lombardia) and four further races (Paris–Nice, Tirreno–Adriatico, La Flèche Wallonne and Paris–Tours). As such, the quality of the races of the ProTour was diminished. The Australian race, the Tour Down Under was added to the calendar, making it the first race outside Europe on the ProTour (although races had previously been held outside of Europe as part of the UCI Road World Cup).
The highly successful U.S. Postal Service ceased operations at the end of the 2007 season. Johan Bruyneel signed on to become the directeur sportif and revamp the embattled Astana; joining him are 2007 Tour de France champion Alberto Contador and 2007 Tour of California champion Levi Leipheimer. Other major signings included American George Hincapie moving to Team High Road and Daniele Bennati from Lampre to Liquigas, while Giro d'Italia winner Danilo Di Luca left Liguigas for the UCI Professional Continental team LPR Brakes–Ballan.
The 2009 UCI ProTour was the fifth series of the UCI ProTour. Two new teams, the American Garmin–Slipstream and the Russian Team Katusha, joined the ProTour, effectively taking over the licenses of Crédit Agricole and Gerolsteiner. Two existing teams changed title sponsors: Team CSC from Denmark became Team Saxo Bank, and Saunier Duval–Scott changed name to Fuji–Servetto. As in 2008, the races organized by the three Grand Tour organizers were not part of the ProTour. Rather than a ranking based only on the ProTour, the UCI designed a World Calendar, on which the Monument events and Grand Tours were included, with a corresponding 2009 UCI World Ranking.
The first race was the 2009 Tour Down Under in January, and the series ended with the 2009 GP Ouest-France in August.