Casilla was signed as a free agent by the Anaheim Angels in 2003. On December 9, 2005, the Angels traded Casilla to the Minnesota Twins for pitcher J. C. Romero. Casilla made his major league debut with the Twins in September of 2006, playing in nine games.

In 2007, after a brief call-up with the Twins, Casilla became the everyday second baseman after Luis Castillo was traded to the New York Mets. Casilla struggled, producing a .222 batting average with no home runs in 189 at-bats.

In 2008, Casilla did not make the Twins Opening Day roster and instead started for the Twins AAA affiliate, the Rochester Red Wings. After an injury to infielder Nick Punto, Casilla was called up in May. On May 19, 2008, Casilla hit a three-run homer, his first career MLB home run against Texas Rangers. It was also his first hit of the 2008 season. Casilla spent the rest of the 2008 season as the Twins' starting second baseman and second hitter in the lineup.

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