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Background  Intestinal parasites still pose major public health problems in developing countries like Ethiopia. Local epidemiological data is indispensable in order to design and monitor prevention and control strategies. Therefore the present study aimed to assess the prevalence of intestinal parasitic infections and associated factors among students at Birbir town, Southern Ethiopia.    Methods  A school-based cross-sectional study was conducted from March to May 2018. Three hundred fifty-one students, who were selected by stratified followed by systematic random sampling, participated in the study. Socio-demographic information was collected using a structured questionnaire. Anthropometric measurements of height and weight were taken at the time of interview. Stool samples were collected and processed by direct wet mount and formol-ether concentration techniques for microscopic detection of intestinal parasites. Data was analyzed using SPSS version 20.    Results  Among 351 (180 male and 171 female) children participated, 135 (38.5%) and 216 (61.5%) were within the age groups of 5–9 and 10–14 respectively. Ninety five (27.1%; 95%CI: 22.2–31.9) of them were tested positive for intestinal parasites. Helminths and protozoa account 21.1 and 7.1% prevalences respectively. Seventy eight children were infected with a single parasite species while 17 were positive for double or triple infections.  A. lumbricoides  (31, 8.8%) was the most frequently detected parasite followed by  T. trichiura  (20, 5.7%) and hookworms (19, 5.4%). Age group of 10–14 years (AOR = 2.51; 95%CI: 1.41–4.45,  p  = 0.002) and absence of hand washing habit after toilet (AOR = 4.49; 95%CI: 2.00–10.1,  p  = 0.001) were significantly associated with intestinal parasitic infection.    Conclusions  The prevalence of intestinal parasitic infection among school age children is still unacceptably high. Age group of 10–14 year old and not having habit of hand washing after toilet were significantly associated with intestinal parasitic infection. The ongoing school based deworming should be strengthened and be integrated with school health programs.    Electronic supplementary material  The online version of this article (10.1186/s12879-019-3879-5) contains supplementary material, which is available to authorized users.

Current status of intestinal parasitic infections and associated factors among primary school children in Birbir town, Southern Ethiopia