The therapeutic effect of clindamycin on Eimeria pragensis (E. pragensis) infection in C57BL/6 mice was demonstrated by suppression of oocyst production and the appearance of degenerated endogenous stages of parasite in the intestine. Short-term clindamycin treatment, from 1 to 4 days or 4 to 8 days post infection (pi) at a dose of 800 mg/kg/day was effective to reduce clinical symptoms, oocyst production and schizogonic development. Interestingly, the short-term treatment schedules allowed the development of a measurable degree of protective immunity to challenge infection in the treated mice. In contrast, clindamycin treatment for the full 12 days period, which almost completely inhibited clinical symptoms and oocyst output, prevented the full development of protective immunity in the treated mice. All these data indicate that clindamycin is efficacious as an anti-eimerian agent and that both early and late endogenous developmental stages of E. pragensis exert a deep influence on the development of effective immunity to challenge infection.