Prior to 2004, Cain was ranked the number two prospect in the Giants' organization (behind Merkin Valdez) by "Baseball America". Cain spent 2004 with two teams. He began the season with the San Jose Giants of the Single-A advanced California League. In 13 starts, he had a 7–1 record, a 1.86 ERA, 89 strikeouts, and 17 walks in innings pitched. In June, he was promoted to the Norwich Navigators of the Double-A Eastern League. In 15 starts, he had a 6–4 record, a 3.35 ERA, 72 strikeouts, and 40 walks in 86 innings pitched. Cain led Giants' minor league prospects in wins, strikeouts, and ERA; he was named the Giants' Organizational Player of the Year.