A vaccine for in ovo vaccination against avian coccidiosis produced by a method including obtaining the coccidial oocysts from a fecal suspension, homogenizing the fecal suspension, separating the oocysts from the fecal debris by either salt flotation using sodium sulfate or gas flotation using air, sporulating the oocysts using hydrogen peroxide and air sparging, bleaching the sporulated oocysts, washing the bleached oocysts, concentrating the sterile washed oocysts and combining the concentrates of various species of coccidial oocysts, and producing a vaccine. The method in whole or in part can be applied to other kinds of encysted protozoa to produce vaccines for various types of animals.