Giles attended Granite Hills High School. He was drafted by the Cleveland Indians in the 17th round of the 1989 Major League Baseball Draft. By 1994, Giles had worked his way up to Triple-A, where he batted .313 for Charlotte making the International League All-Star team. In 1995, Giles was again in Triple-A, where he batted .310 for Buffalo and made his major league debut as a September callup on September 16. He was also an American Association All-Star. Giles hit .355 in 51 games for the Indians in 1996 and hit .314 in 83 games with Buffalo, again making the American Association All-Star team. In 1997, Giles established himself as a major league regular, playing 130 games for the Indians and 112 games in 1998. On November 18, 1998, he was traded to the Pittsburgh Pirates for pitcher Ricardo Rincón.
In 1999 with the Pirates, Giles emerged as a power-hitting outfielder who also hit for average and showed plate discipline. He began a streak of four straight 30-homer seasons, during which he batted no lower than .298 and was named Pittsburgh Pirates Player of the Year each year, and made the National League All-Star team in 2000 and 2001. In addition, he drew a career-high 135 walks in 2002. On August 23, 2003, he was traded to his hometown San Diego Padres for Jason Bay, Óliver Pérez, and minor leaguer Corey Stewart.
From 2004-2006, Giles played in over 150 games each season for the Padres, but in 2006, his batting average dropped to a career-low .263. On May 14, 2006, he drew 5 walks in a game, one shy of the record of 6. In 2007, joined by his brother Marcus, signed as a free agent to be the starting second baseman, Giles batted .271, but missed time with an injured knee. In 2008, Giles, in the third and final guaranteed year of his contract with the Padres, vetoed a potential trade to Boston, citing a desire to remain close to his family.
Giles is a frequent guest on the show Live At Five and he is known by the nickname "Gilly".
Giles is being sued by his former girlfriend for more than $10 million, alleging he battered her while she was pregnant and caused her to have a miscarriage. She alleges Giles began abusing her in 2002. The lawsuit accuses him of hitting and slapping her in the face, shaking and kicking her, and battering her twice when she was pregnant with Giles’ child.