The results of routine screening for intestinal parasites in 1377 refugees and asylum seekers within 2 weeks of arrival in Sweden showed that protozoa, mainly Giardia intestinalis, were found in 235/1377 (17%) and helminths, mainly hookworms, in 264/1377 (19%). Intestinal parasites were more frequently recovered in refugees coming from South East Asia, Africa and Latin America (infection rates 48%, 43% and 42%, respectively) than in those from Eastern Europe (22%) and the Middle East (32%). Refugees who reported gastrointestinal symptoms were less often infected than those without symptoms (p < 0.001). Of the European refugees, 127 came from Bosnia. A high rate of hookworms was found in this group (15%), suggesting that hookworms may also be transmitted in temperate areas under special conditions. We thus identified relatively high rates of pathogens in all groups of refugees. Screening may therefore be recommended, though more for the benefit of refugees than for the prevention of further spread of the infections.