During the 1990s, the protozoan parasites Cryptosporidium and Giardia have emerged as potential waterborne pathogens in the EU. Potable water is not a major route, but there have been some large localized waterborne outbreaks. The infective dose of both the oocytes of Cryptosporidium and cysts of Giardia is low. The diseases are debilitating and may be life threatening for the immuno-compromised.