After the 2002 season, Durham signed a three-year contract US$20.1 million with the San Francisco Giants with a $7 million player option for a fourth year that was later exercised. The health Durham displayed during the earlier years of his career vanished. Between 1996 and 2002, Durham appeared in at least 150 games each season, but in 2003 he only appeared in 110 games and in 2004 he appeared in 120. Recurring hamstring injuries and other injuries caused Durham to spend time on the disabled list. The injuries also hampered Durham's success when he was on the field. Durham's running game and stolen bases dropped as Durham tried to protect his hamstrings from reinjury. Despite these injuries, Durham did post solid offensive numbers during his time in the line up.