The Apicomplexa are a diverse group of intracellular parasitic protists. The majority of species from the classes Coccidea, Haemosporea and Piroplasmea are responsible for widespread diseases of humans and domestic animals. Oocysts of these parasites can persist for long periods of time in the environment (i.e. in water, soil, on vegetation and other food resources), maintaining their infectivity even under harsh environmental conditions and therefore are important for dispersal and transmission to hosts. This review will address the biology, transmission patterns and survival in the environment of Cryptosporidium, Cyclospora and Toxoplasma species, the most common causes of human diseases.