ObjectiveThe aim of this cross-sectional study was to determine the magnitude of intestinal parasitosis and anaemia in a Health Center, North Ethiopia.ResultsA total of 427 outpatients were enrolled and the median age of the participants was 22 years. The prevalence of intestinal parasitosis was 143 (33.5%). Age, place of residence and occupation were significantly associated with intestinal parasitosis. When we see parasite specific factors, significant associations were observed for source of drinking water (P = 0.02), age (P < 0.001) and family size (P = 0.003), respectively with Entameba histolytica, Hookworm and Giardia lamblia infections. The overall prevalence of anaemia was 35 (8.2%). The mean haemoglobin concentration among the study participants was 12.8 mg/dl. The highest prevalence of anemia was recorded for the age group of 15–19 years (29.6%). The proportion of anemia among intestinal parasite -infected and non-infected participants was 10.7 and 7.0%, respectively. Study participants infected with S. stercoralis and hookworm were more likely to develop anaemia than the non- infected ones; AOR (adjusted odds ratio) = 5.3, 95% CI (1.01–27.4); P = 0.028 and AOR = 11.1, 95% CI (3.36–36.9); P = 0.000, respectively.Electronic supplementary materialThe online version of this article (10.1186/s13104-017-2957-2) contains supplementary material, which is available to authorized users.