- Intestinal parasites cause significant morbidity worldwide, particularly in developing populations. At least three pediatric populations reside in southern Israel: the Bedouin population, the general Jewish population and Jewish children of Ethiopian origin. Our aim was to compare intestinal parasites prevalence between the three pediatric populations in southern Israel. This is a retrospective, laboratory, population-based surveillance. Most ova and parasites (O&P) tests in southern Israel (hospital and community obtained) are performed by the hospital parasitology laboratory. All pediatric stool O&P tests examined by the hospital laboratory between 2007 and 2011 were included. Overall, 45,978 samples were examined; 27,354, 16,969 and 1,655 from Bedouin, non-Ethiopian Jewish and Ethiopian children, respectively. 16,317 parasites were identified in 12,325 (26.8%) positive samples. Total prevalences were 36%, 11% and 46% for Bedouin, non-Ethiopian Jewish and Ethiopian children, respectively. Blastocystis hominis, Giardia lamblia and Entamoeba species were the most common parasites identified, constituting ≥80% of positive samples in all groups. Hymenolepis nana was rarely identified in non-Ethiopians Jewish children (0.04% of isolates compared with 2.6% and 0.5% in Bedouin and Ethiopian children, respectively). Other helminthes, excluding H. nana and Enterobius vermicularis, were identified almost exclusively in Ethiopian children ≥5years of age. In conclusion, Bedouin and Ethiopian children were characterized by higher parasites prevalence in stool, compared with non-Ethiopians Jewish children, probably reflecting higher intestinal parasitic disease rates. Certain helminthic infections were identified almost exclusively in Ethiopian children. These differences may be associated with lifestyle differences between the three populations.