A native of Guayama Puerto Rico, Cruz was originally drafted in the 37th round of the 2003 MLB Amateur Draft by the Detroit Tigers but did not sign a professional contract and opted to attend Cumberland University in Tennessee. Cruz was a member of the NAIA champions in 2004 and NAIA runner-up in 2006. While in college he played for the Mankato MoonDogs of the Northwoods League. After his 2006 season at Cumberland, Cirilo was drafted again this time by the Houston Astros in the 27th round of the 2006 MLB Amateur Draft.
He played two seasons in the Astros farm system with Greenville Astros and Tri-City ValleyCats of the Appalachian and New York-Penn Leagues, respectively. Cruz was released by Astros following the 2007 season making him a free agent. Signed by the Rio Grande Valley WhiteWings June 1, 2009, Cruz appeared in 61 games batting .251 with 13 doubles while hitting 10 home runs and driving in 40 runs.