He played in Major League Baseball (MLB) from 2000 through 2009 for the San Diego Padres, Texas Rangers, Philadelphia Phillies, Baltimore Orioles, and Colorado Rockies.

[4] After signing, the Phillies assigned Eaton to their team in the A-level South Atlantic League, the Piedmont Boll Weevils.

[7]1999 saw Eaton climbing his way up the rungs of the Phillies' farm system, starting the year at Clearwater, then earning promotions to Reading and Scranton/Wilkes-Barre.

[6] For his accomplishments, Eaton was honored as the recipient of the Paul Owens Award, given to the top Phillies' minor league pitcher each season.

He posted the best day game ERA in the National League (2.34), and became the third Padres pitcher, after Juan Eichelberger and Doug Brocail, to steal two bases in a single season.

Eaton suffered a bizarre injury when he accidentally stabbed himself in the stomach while trying to open a DVD package with a paring knife,[11] and underwent season-ending "Tommy John" surgery on August 21.

On December 20, 2005, Eaton was traded, along with Akinori Otsuka and Billy Killian to the Texas Rangers for Chris Young, Terrmel Sledge, and Adrián González.

However, during a spring training game on March 29, Eaton injured his right middle finger, causing him to go on the 60-day DL and miss the first half of the season.

[18] On November 27, 2006, Eaton signed a three-year deal worth $24 million to re-join the team that drafted him, the Philadelphia Phillies.

[20] Eaton was the losing pitcher of record when the Phillies lost their 10,000th game in franchise-history[21] on July 15, 2007, to the St. Louis Cardinals, 10–2,[22] marking the first time a professional sports franchise reached that plateau.

Eaton's performance with the Phillies in the first half of the 2008 season was also decidedly poor; through July 12, he notched a 3–8 record in 19 starts with an earned run average of 5.71.

His last two outings before the All-Star break were a prime example; he yielded a combined 17 hits and 14 runs in 61⁄3 innings against the New York Mets and Arizona Diamondbacks.