Beginning in 1999, Choi spent four seasons in the Cubs minor league system and was considered to be one of the organization's top prospects.

He was the Opening Day starter for the Cubs, but suffered a concussion following a collision with teammate pitcher Kerry Wood on June 7, 2003.

With his new team, Choi began the 2004 season impressively batting .295 with nine home runs and 18 RBIs in April.

On July 30, he was traded to the Los Angeles Dodgers along with Brad Penny and minor league pitcher Bill Murphy for Paul Lo Duca, Guillermo Mota, and Juan Encarnación.

However, during the 2005–2006 off-season, DePodesta was fired by Dodgers owner Frank McCourt, and new general manager Ned Colletti signed Nomar Garciaparra to be the everyday first baseman.

Choi represented South Korea in the 2006 World Baseball Classic, in which his most significant contribution was hitting a three-run pinch-hit home run against Team USA.

Choi decided to return home after failing to make Tampa Bay's 40-man roster after 2007 spring training.

[3] Choi finished his first KBO season with a .337 batting average, 7 home runs and 45 RBI, playing in 52 games.

In July, he returned to the 26-man first-team roster, but finished the season with disappointing offensive numbers, batting .229 with only 6 home runs and 22 RBI.