In recent decades, apple cider has been implicated in a series of outbreaks of foodborne illness. The objective of this study was to determine the presence and concentrations of pathogenic and indicator microorganisms in apple cider processed in Michigan and to evaluate the impact of thermal pasteurization, UV light radiation, and implementation of hazard analysis critical control point (HACCP) plans on these microbes. Cider samples were obtained from Michigan mills between 1997 and 2004 and analyzed for Escherichia coli O157:H7, Salmonella, generic E. coli, total coliforms, and aerobic bacteria. Neither E. coli O157:H7 nor Salmonella were detected in any tested cider samples, suggesting a very low frequency of pathogens in Michigan apple cider. The persistent and relatively high frequency of generic E. coli observed in samples obtained in all years indicates a continued risk of pathogen contamination in Michigan apple cider, especially when it is untreated. The use of thermal pasteurization or UV light radiation and reported implementation of HACCP plans were associated with lower frequency and counts of generic E. coli, total coliforms, and aerobic microorganisms. However, the relatively high counts of indicator organisms in some cider samples that were claimed to be treated according to these pathogen reduction measures indicates that some processors had inadequate practices, facilities, or equipment for pathogen reduction or did not consistently or adequately apply practices or pathogen-reduction equipment in an effective manner.