The prevalence of intestinal parasites in young Quichua children was assessed in 20 rural communities in the highlands of Ecuador in August 2005. The caregivers of 293 children aged 12-60 months were interviewed about the status of child health, household socioeconomic and environmental factors, and water-use practices and were requested to collect a faecal sample from the study child. Two hundred three (69.3%) of the 293 children provided faecal samples that were tested for parasites. The overall prevalences of infection for specific agents were Entamoeba histolytica or dispar 57.1%, Ascaris lumbricoides 35.5%, Entamoeba coli 34.0%, Giardia intestinalis (lamblia) 21.1%, Hymenolepis nana 11.3%, Cryptosporidium parvum 8.9%, Chilomastix mesnili 1.7%, Hymenolepis diminuta 1.0%, Strongyloides stercoralis 0.7%, and Trichuris trichiura 0.5%. The prevalence of parasites increased with age. Water storage, water treatment, consistent latrine-use, and participation in a community-based clean water project were not strongly associated with the prevalence of intestinal parasites, although having dirt floors was a risk factor for infection with E. histolytica or dispar and G. intestinalis.