Ellsbury began the 2006 season ranked as the sixth-best prospect in the Red Sox' organization according to Baseball America. He started the season with the Wilmington Blue Rocks of the Class A-Advanced Carolina League. On July 3, he tied a Wilmington franchise record by stealing four bases in a game. After batting . 299 with 25 steals in 61 games and being named to the 2006 Carolina League All-Star team, Ellsbury was promoted to the Portland Sea Dogs of the Class AA Eastern League on July 12. Soon after his promotion to Portland, Ellsbury was named Eastern League Player of the Week for August 6–13, after batting . 400 along with a home run, and hitting safely in seven straight games. Ellsbury finished the season in Portland batting . 308 with 16 steals in 50 games and the Red Sox selected him as their Minor League Defensive Player of the Year and Base Runner of the Year. They assigned him to the Peoria Javelinas of the Arizona Fall League (AFL), an off-season developmental league for top prospects. In the AFL, Ellsbury hit . 276 in 25 games, and his defensive skills were enough to earn him a spot in the AFL Rising Stars All-Star game.