In, Trachsel began his professional career with the Short-Season Geneva Cubs and the Class-A Advanced Winston-Salem Spirits. He went a combined 5-4 with a 3.27 ERA in 14 games, all for starts. Trachsel was promoted to the Double-A Charlotte Knights of the Southern League in. Trachsel went 13-8 with a 3.06 ERA and 135 strikeouts in 29 games, all for starts.
Chicago Cubs
He began the season with the Triple-A Iowa Cubs where he went 13-8 with a 3.95 ERA and 135 strikeouts in 27 games, 26 starts. Trachsel was promoted to the Major Leagues in September and made his debut on September 19 against the Florida Marlins going seven innings with five strikeouts while giving up two earned runs and taking the loss. Trachsel would play most of the season with Chicago, pitching just two games in Iowa going 0-2 with a 10.00 ERA. His Minor League stats were much better however as he went 9-7 with a 3.21 ERA in 22 games, all starts. He also had one complete game and struck out 108 total over the season. In Trachsel spent his first full season at the Major League level. He went 7-13 with a 5.15 ERA, 117 strikeouts and two complete games in 30 games, 29 starts. Trachsel was named to the Major League Baseball All-Star Game and posted a career-best 3.03 ERA in. He also finished the season with a record of 13-9 with two shutouts, three complete games and 132 strikeouts in 32 games, all starts. His first shutout was a one-hit game against the Houston Astros on May 14 where he surrendered the only hit on a lead-off double to Brian Hunter. He also pitched two games with the Double-A Orlando Cubs where he went 0-1 with a 2.77 ERA. In Trachsel started a career-high 34 games with the Cubs, a record he has tied twice. He went 8-12 with a 4.51 ERA and 160 strikeouts. He led the National League in home runs allowed and was second in hits allowed. He had a record of 15-8 in with an ERA of 4.46, 149 strikeouts and one complete game. Also in 1998, on September 8 Trachsel allowed Mark McGwire's record breaking 62nd home run, breaking Roger Maris' longtime record of 61. McGwire hit the pitch 341 feet over the left field wall, his shortest of the year. McGwire went on to hit 70 home runs that year. Additionally, he was the starting and winning pitcher in the Cubs' 5-3 Wild Card tie-breaker game victory over the San Francisco Giants, giving up just one hit through six-plus innings. In, his ERA rose to a career-worst 5.56, his 18 losses were two worse than any pitcher that season and the Cubs let him go.
Trachsel split the season between the Tampa Bay Devil Rays and Toronto Blue Jays in the American League, accumulating 15 losses between the two teams.
New York Mets
Trachsel's beginning with the New York Mets in was so poor that he was sent to the minor leagues. Upon returning to the Mets, his career was reborn. He finished 2001 well and continued to shine in when he had a 3.37 ERA. His success continued with 16 wins in. Trachsel was even named the National League Player of the Week on August 25, 2003, following a 16.1 inning span in which he allowed no walks, no runs and only six hits. However, after starting well in, he suffered a herniated disc in his back, the first major injury of his career, which also cost him much of the. He underwent a microdiscectomy in March 2005 and returned for the final six starts of the season, posting a league-average 4.14 ERA and going 1-4. In, Trachsel recovered to start 30 games and tied Tom Glavine for the team lead with 15 wins, despite an earned run average near five. On September 18, 2006, he had one of his best performances of the season as the Mets clinched the National League Eastern Division Championship. He pitched 6⅓ innings, allowing three hits and three strikeouts in the 4-0 win over the Florida Marlins. He also started the clincher of the NLDS, but was shaky and removed in the 4th inning. In Game 3 of the NLCS, he gave up five runs in just one inning before being hit by a hard ground ball. The Mets lost the game 5-0.
