As an amateur, Ivan Basso finished second in the 1995 junior World Championships and his first big result was winning the U-23 World Championships in 1998. In his youth he fiercely competed with fellow Italian riders Giuliano Figueras and especially Danilo Di Luca who proclaimed he would have won the U-23 World Championship himself had it not been for the team tactics. Before Basso could turn professional, his parents wanted to see him finish his Technical Geometry studies. He turned professional with Risso-Scotti Vinavil in 1999, where he rode his first Giro d'Italia. He did not finish the three-week race, but he made it a priority to win it some day. In 2000 he moved to Amica Chips where he won his first professional victories in the 2000 Regio Tour.

In 2001, he moved to Fassa Bortolo under the guidance of sporting director Giancarlo Ferretti. He scored several notable victories in 2001, and he made his Tour de France debut in the 2001 edition. His attack on the Bastille Day stage prompted a five man break-away which rode for the victory, but Basso crashed on a mountain descent and was forced to abandon the race.

His next two years were devoid of significant wins, even though he had promising rides in the Tour de France. In the 2002 edition of the Tour de France, Basso finished 11th overall and won the white jersey, the award presented to the best-placed rider in the general classification under the age of 25.

Tour 2003: Basso during stage 12 (ITT). He finished 20th on the day and lost 4:24 to eventual winner Lance Armstrong.He impressed again in the 2003 Tour, finishing seventh overall in spite of receiving little help from his Fassa Bortolo team-mates who, after dedicating their efforts in the first part of the race to help Alessandro Petacchi win four stages, had to pull out due to food poisoning, leaving only two riders to help Basso. Despite his good results as the best placed Italian rider in the Tour de France, he was behind fellow Italian teammate Dario Frigo in the Fassa Bortolo pecking order for the biggest race in Italy, the Giro.[2] After the promising start to his Fassa Bortolo career, Basso's relationship with Giancarlo Ferretti turned sour. Basso failed to respond well to the management methods of the "iron sergeant" who thought Basso did not win enough races.

Apart from the individual time trial stages, Basso had only lost around a single minute to the winner in the 2003 Tour, and he was not short of new team offers. Despite strong rumors sending him to team U.S. Postal Service, Ivan Basso moved to Team CSC for the 2004 season, under guidance of team manager Bjarne Riis. At Team CSC, Basso was to fill the role as team captain, which Tyler Hamilton had left vacant at the Danish outfit, with the main aim to be a challenger in the Tour de France. Ivan Basso's weakness was the time trial and before the 2004 season he and teammate Carlos Sastre trained in a wind tunnel at the Massachusetts Institute of Technology to improve their aerodynamic positioning on the bike. The time trial skill of Ivan Basso was one of the main points of improvements over the next years.

Tour 2004: Basso (left) and Armstrong at Basso's stage 12 win at La Mongie.Basso looked impressive in the 2004 Tour de France, winning stage 12 ahead of eventual winner Lance Armstrong, his first victory since 2001. Due to his relatively poor time trial results, he only finished 8th on the stage 16 time trial up the mountain Alpe d'Huez, where he was caught and passed by Armstrong, and 6th in the stage 19 time trial. In all, he lost a combined 5 minutes and 13 seconds in the two stages. His time loss on the last time trial effectively sent Basso down to third place behind Andreas Klöden, and Basso finished 6:40 behind overall winner Armstrong. When Ivan Basso learned, during the 2004 Tour, that his mother had pancreatic cancer, Armstrong was a personal support of Basso, as he had survived cancer himself. Basso held his daughter in his arms as he was honored in Paris and was resilient about his chances of a future Tour win. He ended the season, participating with the Italian national team in the 2004 World Championships in Verona, helping fellow Italian Luca Paolini get a Bronze Medal. In the off-season, Team CSC was in a financial struggle. Even as Bjarne Riis let riders leave who received superior offers from other teams, Basso did not move to team Discovery Channel even though an economically more lucrative contract was proposed.

January 2005 saw the death of Ivan Basso's mother, who died from the cancer. Ivan Basso went on to focus on the 2005 Giro d'Italia, in her memory, as his main aim for that season. By both focusing on winning the Giro and the Tour, he was going against the trend of only aiming for one big race a season, a tactic most notably employed successfully by Lance Armstrong. Basso wore the leader's jersey, the maglia rosa, in the Giro until severe stomach problems caused him to lose the lead on stage 13. He lost another 40 minutes during the 14th stage, a mountain stage which included the Stelvio Pass, and thus effectively ended his bid for overall honors. No longer dangerous to the other main riders, Basso decided to continue in the race with the objective of winning stages which he did manage during stage 17 a mountain stage. He also won the 18th stage, a time trial, ahead of team mate David Zabriskie, demonstrating the improvement he had made in this area.

Tour 2005: Basso after stage 20 (ITT). He finished 5th on the day and remained 2nd overall on the GC.At the 2005 Tour de France, he started out comparatively weakly on stage 10, the first mountain stage of the race, where he trailed the front group by a minute. But for the rest of the race, Ivan Basso was once again the only rider to keep up with the race leader Lance Armstrong in the mountains, and on occasion he tried to pressure the eventual winner by going on the attack. Basso was still weaker in the time trials, although he had improved significantly when compared to 2004. He lost a collective 3:47 over two time trial stages, as Basso placed second overall in the Tour, 4:40 behind Lance Armstrong. During the 2005 Tour de France, Basso signed a new 3-year contract with CSC running up to 2008, ending speculation that he might defect to Discovery Channel to take over after the retiring Lance Armstrong.

Following his overall rank of 28th in the 2005 Giro, Basso returned to the Giro in 2006 with the intention to win. Following a good performance in the stage 1 time trial, Basso and his CSC teammates won the 5th stage, a team time trial. Basso's first solo stage victory came on the 8th stage, the first mountaintop finish of the Giro, where he countered an attack by Damiano Cunego and rode to the finish by himself. That victory also allowed him to gain enough time on his rivals to put him in the maglia rosa leader's jersey for the first time in the 2006 Giro, a jersey which he would hold on to for the remaining 13 stages.

Stage 11 was a long and flat individual time trial where Basso finished in second place, losing only to former two-time World Time Trial Championship winner Jan Ullrich, beating riders like the Italian national time trial champion Marco Pinotti. During the last week of the 2006 Giro, Basso became truly dominant, as he consistently beat his main rivals for the General Classification, and won stages 16 and 20 along the way. His victory in Stage 20, where he rode to a solo victory on the final ascent into Aprica, was notable when he, already sure of his victory, pulled out a picture of his newly born son Santiago, and held it aloft as he crossed the finish line. Santiago Basso had been born the previous day, and Basso had not yet seen his son in the flesh, having been given the picture only hours before the stage started. Basso eventually finished 9 minutes 18 seconds up on the second placed rider, José E. Gutierrez Cataluna, the largest margin of victory in the Giro d'Italia since 1965. After the last stage of the 2006 Giro d'Italia, Basso declared that he would continue along his pre-season plan to also ride the 2006 Tour de France.