A two-year evaluation of Giardia and Cryptosporidium cyst removal through direct filtration and conventional treatment, sponsored by the USEPA, was conducted by the Utah Department of Environmental Quality. Cysts were seeded in a spike at a full scale water treatment plant, and continuously in a step dose at a pilot plant; both operated under conventional treatment and direct filtration regime. Sampling before and after treatment was conducted using 2.0 um membrane filtration. Cysts were detected using Percoll flotation in 15 mL tubes and IFA staining on 2.0 um porosity polycarbonate membrane filters, and enumerated using epifluorescent microscopy. The results of 8 cyst seeding trials, conducted at a 900 gpm treatment plant, and 20 trials, conducted in a 0.5 gpm pilot plant, indicated that raw water quality (turbidity and algal content), as well as treatment effectiveness in removing turbidity, controlled the removal of seeded Giardia and Cryptosporidium cysts. Changes in raw water quality, observed between the seeding trials, influenced removal rates more than the mode of treatment. Higher removal rates were consistently observed for Giardia cysts (3.1-log) than for Cryptosporidium oocysts (2.6-log). A high correlation was found between cyst removal rates and removal of the respective size particles; poorer between the cysts and turbidity removal, while no correlation was established between the removals of cysts and heterotrophic bacteria.