Three 13- to 18-day-old whooping cranes (Grus americana) and a 9-year-old whooping crane died in outdoor pens at the Patuxent Wildlife Research Center. The deaths were associated with an overwhelming systemic infection by an intracellular protozoan parasite, which resulted in enteritis, granulomatous bronchopneumonia, hepatitis, splenitis, and myocarditis. The clinical, histopathologic, and electron microscopic findings were similar to those in sandhill cranes (Grus canadensis) at the Patuxent Center found to be infected with Eimeria reichenowi and E gruis. Since these eimerian species also parasitize wild whooping cranes, this parasite might be an important pathogenic agent for this species.