In 2001, Anderson had career highs in wins (9), games started (34), innings pitched (206.1) and strikeouts (89).

In 2002, Anderson regressed and lost control, walking 63 batters while striking out just 47 in 140+2⁄3 innings for the Pirates.

[1] Anderson later signed a minor league deal with the Giants, for which he started 8 games, going 1–4 with a 6.44 ERA.

Anderson was traded to the Boston Red Sox for a minor league pitcher on July 2, 2004.

In 2005, Anderson pitched in the Twins, Astros, Cubs and Devil Rays minor league systems.