Globally, Cryptosporidium infection continues to be a significant health problem where it is recognized as an important cause of diarrhoea in both immunocompromised and immunocompetent people. In developing countries persistent diarrhoea is the leading cause of death in children younger than five years of age, where it accounts for 30 to 50 percent of those deaths. Encouragingly an increasing number of investigations in developing countries employ molecular tools, significantly improving the quality of epidemiological information. This improved Cryptosporidium monitoring, with appropriate molecular methods, in surface water, livestock, wildlife and humans, will increase current knowledge of infection and transmission patterns, and ultimately help to control Cryptosporidium via improved risk assessments in the future.