[4] For his contributions, Fontenot was named the National Freshman of the Year by the Southeastern Conference; The Sporting News; and Collegiate Baseball, which declared him a co-winner.

[5] Fontenot was a part of the NCAA team that played well enough during the season to advance to the Baton Rouge Regional.

Along with future Chicago Cubs teammate Ryan Theriot, Fontenot was a member of the LSU Tigers baseball team that won the 2000 College World Series.

In the NCAA Baseball Tournament, Fontenot recorded a team-high batting average of .432 with four doubles, two home runs, and nine RBIs.

[2] Though he had only played two years of college baseball, Fontenot's age made him eligible for the 2001 MLB Draft.

In 126 games, he batted .325 (second in the league to Alex Ríos's .352) with 146 hits (ninth), 12 home runs, and 66 RBIs.

In 136 games (tied with Earl Snyder for fourth in the league behind Bry Nelson's 142, Víctor Díaz's 141, and Jhonny Peralta's 138), he batted .279 with 146 hits, eight home runs, 49 RBIs, and 10 triples (tied for second in the league with John Rodriguez and Pete Orr behind Mark Budzinski's 15).

On February 3, 2005, he was traded to the Chicago Cubs along with second baseman/outfielder Jerry Hairston Jr. and right-handed pitcher Dave Crouthers for outfielder Sammy Sosa.

[15] He made his major league debut in the first game of a doubleheader on April 13, 2005, pinch-running for Aramis Ramírez and scoring a run in the team's 8–3 loss to the San Diego Padres.

[1][16] Fontenot played in four games with the club (pinch-hitting in the other three) before getting sent back to Iowa on April 23 to make room for Ben Grieve on the roster.

[17][18] He was also called up on May 13 and played three further games for Chicago, pinch-hitting in two and pinch-running in one, before getting sent back to Iowa on May 20 when pitcher Joe Borowski came off the disabled list.

[9] In 2006, Fontenot spent the entire season with Iowa, batting .296 with 107 hits, eight home runs, and 36 RBIs in 111 games.

[21] Pinch-hitting against the New York Mets on May 15, he got his first major league hit, a double against Ambiorix Burgos in Chicago's 10–1 triumph.

[1][23][24] He hit his first major league home run against Buddy Carlyle on June 10, in a 5–4 loss to the Atlanta Braves.

[23][27][28] After the month of June, he only batted .214 for the rest of the season, losing the starting second base job to DeRosa in mid-August.

[30] Though used mostly as a bench player in 2008, Fontenot also started 49 games, many of which were in June and July while Alfonso Soriano was on the disabled list.

[31][32] On May 3, he had three hits and set a career high with four RBIs, including a three-run home run against Kyle Lohse in a 9–3 victory over the St. Louis Cardinals.

[1] He had the first pinch-hit home run of his career on August 28 against Ryan Madson, starting a five-run rally for the Cubs in their eventual 6–4 triumph over the Philadelphia Phillies.

[30] Entering the 2009 season, the Cubs traded DeRosa and signed infielder Aaron Miles to a two-year contract.

However, manager Lou Piniella named Fontenot the team's starting second baseman on March 14 during spring training.

[37][38][39] On April 8, he had four RBIs, including a three-run home run against Russ Ortiz in an 11–6 victory over the Houston Astros.

[1][41] After batting .230 through August 7, Fontenot lost his position as the Cubs everyday second baseman, splitting time with Jeff Baker for the rest of the year.

The 2009 season was a year of career highs for Fontenot in games (135), at bats (377), hits (89), home runs (nine, same as in 2008), and RBIs (43).

Fontenot was in a tie for the last spot with Adam Jones and Micah Owings, but he won the tiebreaker because he played more games in 2008 than the other two.

[47] San Francisco wanted him because Édgar Rentería had just been placed on the disabled list with a left biceps strain.

[1] After a one-year hiatus, Fontenot returned to the playoffs as part of a Giants team that won the NL West.

He had a triple against Tim Hudson to start the second inning of Game 3 and scored the Giants' first run in their eventual 3–2 victory.

[59] On April 13, Fontenot hit a go-ahead home run against Ted Lilly to help the Giants win 4–3 over the Dodgers.

[60] He took over as the Giants' everyday shortstop on April 30 after Pablo Sandoval was placed on the disabled list with a broken hamate bone and Miguel Tejada was shifted over to play third base.

[66] He was assigned to the Lehigh Valley IronPigs of the International League, batting .308 with one home run and seven RBIs in 16 games with the club.