A graduate of Mar Vista High School in Imperial Beach, California, Loaiza was signed by the Pittsburgh Pirates as an undrafted free agent on March 21, 1991. With the Gulf Coast Pirates in the Rookie leagues he started five games in 1991, finishing with a 5–1 record and a 2.26 ERA. He moved through the Pirates farm system with stops at Augusta (class A - 1992), Salem (class A - 1993) and Carolina (class AA - 1993-1994). He also played for the Mexico City Red Devils of the Mexican Summer League during the 1993 season.