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Several factors including socio-economic and access to health facility influence burden of intestinal parasites. Epidemiological data from hard to reach areas will help to identify high-risk communities for targeted intervention. We, therefore, assessed the magnitude of intestinal parasites among Zay people residing in three islands of Lake Ziway in Ethiopia. This cross-sectional survey was conducted in March 2013 on 444 individuals aged 6 months to 85 years. Stool samples were analyzed using wet mount and formol-ether concentration methods. Data were collected using interviewer-administered questionnaire and analyzed using STATA version 10. Among the study participants, 52% (321/444) were children under 15 years. While 72.8% were positive for at least one intestinal parasite, single, dual and triple infections were found in 42.1%, 23.9% and 6.3%, respectively. Four types of intestinal parasites were detected in two children. The commonest parasites were Entamoeba histolytica/dispar (51.4%), Schistosoma mansoni (17.8%), Giardia lamblia (14.4%), Trichuris trichiura (10.8%), Taenia species (5.6%), Hymenolopis nana (4.5%), Ascaris lumbricoides (4.1%), Entrobius vermicularis (0.9%), Hookworm (0.7%), and Strongyloides stercoralis (0.2%). Remarkable proportion of study participants (51.3%) had no latrine and >85% of the islanders use the lake water for drinking, cleaning or both. About 36% had no information about waterborne and related diseases, while 31% never heard about bilharziasis. Fishing and farming were the main source of income. In the multivariate model, being in the age group > 15 years (AOR = 0.49; 95%CI = 0.28-0.85) and not using lake water for drinking or washing (AOR = 0.52; 95%CI = 0.28-0.99) had protective effect, after adjusting for education, occupation and hand wash after latrine use. The observed high rate of intestinal parasites (72.8%) in these hard to reach Islanders of Lake Ziway, warrants targeted and sustainable intervention.