He made his major league debut on June 30, 1999, during a 14–5 loss against the Oakland Athletics, allowing three earned runs in an inning of work.

[7] In 2003, he enjoyed his most successful big league season, where he went 4–2 with a 1.58 ERA in 79.7 innings pitched where he struck out a career high 87 batters.

[8] On December 8, 2005, the White Sox traded Marte back to the Pittsburgh Pirates in exchange for Rob Mackowiak.

[9] Marte made three relief appearances in the World Baseball Classic for the Dominican Republic in 2006 but was shut down after experiencing shoulder inflammation.

On July 26, 2008, Marte and Xavier Nady were traded to the Yankees in exchange for José Tábata, Ross Ohlendorf, Jeff Karstens, and Daniel McCutchen.

After a shaky first outing in Game 2 of the 2009 American League Division Series, in which he surrendered two consecutive singles to the Minnesota Twins before being relieved, Marte retired all twelve of the remaining batters he faced during the postseason.

During Game 6 of the 2009 World Series, Marte faced Philadelphia Phillies stars Chase Utley and Ryan Howard, striking out both of them on the minimum six pitches.