He played in MLB for the Philadelphia Phillies, Minnesota Twins, St. Louis Cardinals, Boston Red Sox, Los Angeles Dodgers, and Oakland Athletics.

[5] In 2002 with the Scranton/Wilkes-Barre Red Barons, Punto played in 115 games and hit .271 with a home run, 29 RBI and 42 stolen bases, earning a selection as an International League All-Star.

[7] After playing in 64 major-league games in 2003, Punto was acquired by the Minnesota Twins on December 3, 2003, along with Carlos Silva and Bobby Korecky for Eric Milton.

Punto was one of four Twins players nicknamed "the Piranhas" by then Chicago White Sox manager, Ozzie Guillén.

[5] In 2007, Punto experienced his statistically worst full season with Minnesota, batting .210 with a home run and 25 RBI 150 games.

Punto also posted a −27.1 VORP in 2007, 8.5 runs worse than the second-worst position player in baseball, White Sox infielder Andy González.

After returning from the disabled list, Punto was re-inserted into the regular lineup at second base, following the struggles of infielders Alexi Casilla and Matt Tolbert.

In July, he was essentially replaced as the starter at third base by Danny Valencia, but he continued to play regularly due to injuries to Orlando Hudson and J. J. Hardy.

[15] He played in 63 games with the Cardinals as a utility player, and hit .278 with a career high .388 on-base percentage, a home run and 20 RBI in 133 at bats.

[5] On August 25, 2012, Punto was traded to the Los Angeles Dodgers (along with Josh Beckett, Carl Crawford and Adrián González and $11 million in cash) for James Loney, Iván DeJesús, Jr., Allen Webster and two players to be named later (Jerry Sands and Rubby De La Rosa).

[20] On November 13, 2013, Punto agreed to a one-year, $3 million contract with the Oakland Athletics, that included a vesting option for 2015.

[23] On January 7, 2015, Punto signed a minor league contract with the Arizona Diamondbacks that included an invitation to spring training.

[24][25] However, on February 20, Punto informed the Diamondbacks that he would not be reporting to spring training and would be taking the year off from baseball, though he was not officially retiring.