Waterborne protozoal disease is one of parasitic diseases which are caused by protozoa,transmitted via water.In recent years,a large number of diseases outbreak due to protozoa from contaminated water have raised serious concerns about the waterborne protozoal disease.This paper reviews the advance of the study on epidemiology and molecular detection of waterborne protozoon such as Cryptosporidium,Giardia and Cyclospora at home and abroad.