The primary objective of this study was to gain information about the relative effectiveness of different filtration media for the removal of cysts and oocysts. The additional objectives of this study are to determine the absolute removal efficiencies for the different filtration media; to evaluate the potential applicability of aerobic endospores, particle counts, turbidity, and polystyrene beads for use as surrogates for cyst and oocyst removal; and, to assess the reproducibility of such studies. The approach used to accomplish these objectives was to spike heat inactivated, antibody preserved Giardia muris cysts and Cryptosporidium parvum oocysts into influent water to pilot-scale filters. Three of the filters were filled with granular media and one of the filters was empty. Influent and effluent samples were analyzed for protozoa, turbidity, particle counts, and endospores. The removal of polystyrene beads was also examined in one run. Three identical runs were studied under winter conditions, and three identical runs were examined under summer conditions.