Pérez was signed by the San Diego Padres as an amateur free agent in 1999. He made his debut with the Padres in 2002. Pérez did well for a rookie after being called up by the Padres in 2002, striking out over a batter per inning, but he suffered from control issues at times. He regressed somewhat in 2003.

In August 2003, Pérez was sent by San Diego to Pittsburgh along with Jason Bay and Cory Stewart in the same trade that brought Brian Giles to the Padres.

Before the 2004 season, the team overhauled his pitching mechanics. His average of 10.97 strikeouts per nine innings was highest in the Majors (239 SO/196 IP); his 2.98 ERA was fifth in the National League (tied with Roger Clemens); and his 12–10 record could have been ever better with reasonable run support early in the season. Pirates' bats provided two or fewer runs in Pérez' 16 starts before All-Star break, causing him to post a 5–4 record with five no decisions despite a 3.24 ERA. In that season, Pérez pitched at least six innings and allowed three or fewer runs in 21 of his 30 starts (70%). Through this first three seasons, Pérez had compiled a 20–25 record with 474 strikeouts and a 3.86 ERA in 412.2 innings. His 239 strikeouts that year are currently the third-most in a season by a modern-day Pirate, trailing only Bob Veale's 276 in 1965 and 250 in 1964.

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