The 2009 Tour began, as have many in the past, with an individual time trial, but instead of a very brief prologue, this 15 kilometer ride saw the race's overall favorites show themselves on day one. The favourite for the stage, Fabian Cancellara, won with Alberto Contador coming in second. Time-trial specialist Bradley Wiggins came third.
This stage was largely flat, but had one third category, and three fourth category, climbs in its first 129km, and most of the last 15km was downhill. A four man breakaway (Stéphane Augé, Stef Clement, Cyril Dessel and Jussi Veikkanen) held a maximum advantage of some 5 minutes, but they were caught with 10 km remaining, initially by Mikhail Ignatiev, and shortly after by the rest of the peloton. Ignatiev was caught with 5 km left, and some of the riders shaping to contest the sprint were disrupted by a crash and a missed turn in the last kilometre, allowing Mark Cavendish a clear win.
 This was the first team time trial in the Tour since 2005. Riders finishing with the first five members of their team all received the same time: riders who became isolated from their team recorded an individual time. The time trial was won by Astana, beating Garmin-Slipstream, who rode about half the race with only 5 riders left, by 18 seconds. Fabian Cancellara and Team Saxo Bank took 40 seconds longer than Astana, Cancellara thus having the same overall time as Lance Armstrong but retaining the yellow jersey by virtue of the fractions of a second recorded in the opening time trial.
The Tour visited Cap d'Agde for only the second time ever, as the early Tour flat stages continued. Perpignan, on the other hand, is a traditional city for the Tour to visit, thought to symbolically indicate the Tour's entrance to (or exit from, in "counter-clockwise" years) the Pyrenees. A six rider breakaway, consisting of Anthony Geslin, Yauheni Hutarovich, Mikhail Ignatiev, Marcin Sapa, Albert Timmer and Thomas Voeckler, formed within the first kilometre, and achieved a maximum lead of more than nine and a half minutes. Attacks by Ignatiev in the last 10km had reduced the escape group to four, until with 5 km Voeckler made what proved to be the decisive break. Ignatiev finished second just in front of Cavendish and the rest of the pack.
During the race, the peloton had split into several groups as a result of the wind, as had happened two days before. Among the absentees in the first group of the peloton were Denis Menchov and Tom Boonen, but they and their group managed to return to the main group after several kilometres of chasing. Robert Gesink, who had crashed just before the windy passage along the coastline started, eventually had to let the peloton go and finished more than nine minutes behind with what in the end proved to be a broken wrist. 
This last flat stage before the 2009 Tour entered the Pyrenees took place entirely within Spain, on a course that is frequently used in the Tour of Catalonia. The main break of the day was instigated by David Millar after 46km, and he was joined by Stéphane Augé, who took the King of the Mountains leadership, and Sylvain Chavanel, and eventually by Amets Txurruka. Millar, 10th at the beginning of the stage, was virtual leader of the tour for much of the day, as the lead extended to 3'45", and he attacked and left behind his fellow escapees with 29km remaining. The uphill approach to the finish on Montjuïc did not suit some of the sprinters, but there was a group of about 60 at the head of the field when Millar was caught near the 1km red flag, and with some GC contenders and climbers contesting the finish, Thor Hushovd emerged as stage winner. The day was marked by numerous rain showers, and a number of falls, with Michael Rogers the main overall contender to lose considerable time.
This second stage in a row that did not visit French soil was both the longest stage, and the highest finish of this year's tour. The first key break of the day comprised three riders, and escaped after 8 km of cycling, but it was joined by a six man chase group shortly after the first of the day's minor climbs, but this was the day on which the race reached the high mountains. The escapees stretched their advantage to more than 14 minutes before reaching the major climbs, but as they included Rinaldo Nocentini, who was 32nd in the general classification and only 3'13" behind the yellow jersey, the peloton, driven by the Astana squad, made a chase. Although the lead was greatly reduced, all but one of the escapees finished before the elite riders, and Nocentini retained a big enough advantage to take over the race leadership. Brice Feillu attacked the other four escapees who were at the head of the field with 5.5 km remaining, and stayed away to claim his first professional win in his first Tour de France. After an attempted attack on the other contenders for the Tour victory by Cadel Evans, 2007 winner Alberto Contador made a successful attack on the elite group with 3 km to go, beating them to the line by 21 seconds, and taking second place overall, while after five days in the yellow jersey, Cancellara finished more than nine minutes behind the stage winner, having been dropped on the final climb.
The Tour returned to France in the second of three Pyrenean stages, which featured three categorized climbs, including the imposing Port d'Envalira at just over 2,400 meters, before a steep descent. A number of early breakaways, including one featuring Cadel Evans, and one that enabled Thor Hushovd to take sufficient points in intermediate sprints to claim the green jersey, came to nothing, and by the top of the final climb three riders, Mikel Astarloza (later suspended for EPO use), Vladimir Efimkin and Luis León Sánchez, were at the front of the race, with an array of chasers and struggling former members of breakaways between them and a group that included all the GC contenders and the yellow jersey wearer, Nocentini, who was part of a group, also including Denis Menchov, that had recovered a 30 second deficit on the elite group shortly before the top of the climb. Meanwhile, Caisse d'Epargne leader and 2006 Tour winner, Óscar Pereiro, became the highest profile rider to abandon the race. On the 42 km descent, Sandy Casar caught the three leaders, and this group of four maintained a comfortable lead over the peloton, and the race among these riders was triggered when Efimkin broke clear with 4km remaining, a move that at one stage looked as though it might succeed, but he was caught by the other three escapees just before the red kite, and Sánchez won the sprint from Casar. There was no change to the position of the race favorites.
The Pyrenees portion of the 2009 Tour ended with this stage which had two categorized climbs, the Col d'Aspin and the Col de Tourmalet and, as the previous day, a lengthy flat stretch before the finish, essentially neutralising the stage in terms of challenges relevant to the overall classification. An early break of twelve riders became thirteen after extensive effort by the Liquigas squad to get Franco Pellizotti across the divide. After not much more than half an hour, the escape group was reduced to four: Pellizotti, Jens Voigt, Pierrick Fédrigo and Leonardo Duque, who was dropped on the climb of the Col d’Apsin, while a chase group of 9 riders formed behind, including Egoi Martínez, who was to gain enough points over the cols to take the polkadot jersey at the end of the day. By the top of that mountain, the leading trio held an advantage of 2'45 over the counter-attack and 3'30 over the peloton; at the top of the Tourmalet only Pellizotti and Fédrigo remained at the front, with seven surviving chasers at 2'40 and the peloton at 5'05. The descent and flat run in saw all the escapees except the two leaders reeled in, as Rabobank and Caisse d'Epargne sought to engineer an opportunity for their sprinters, but Pellizotti and Fédrigo held on to contest the stage win between themselves, the Frenchman emerging as victor.
The Bastille Day stage, one of two stages on which it was intended riders will not be in radio contact with their team cars, was flat, heading to Issoudun for the first time on the Tour de France. The day's break was initiated by Thierry Hupond in the second kilometre, and he was joined by Mikhail Ignatiev and Benoit Vaugrenard, and after a hold-up at a level crossing, by Samuel Dumoulin. The group's lead never reached four minutes, but over the latter stages the peloton found the gap slow to close. The catch was finally made with a little over 1½ km left, Hupond being the last member of the breakaway to yield to the chasers, and Team Columbia-HTC's train again delivered Mark Cavendish for a win in the sprint, ahead of Thor Hushovd, who retained the green jersey. It was initially announced that a split in the field meant that most of the peloton, including Levi Leipheimer and Bradley Wiggins, two of the top five in the overall classification at the beginning of the day, lost 15 seconds to the first 52 finishers, but this was rescinded the following day.
This was another flat stage, with a two man breakaway, consisting of Johan Van Summeren and Marcin Sapa, which reached its largest advantage of 4'45" after 45 km and was caught with 5 km remaining. Mark Cavendish again dominated the sprint, taking his fourth stage of the tour and regaining the green jersey.