A cross-sectional study was carried out to determine the prevalence of intestinal parasites in primary school children in Bandar Abbas, southern Iran during January to March 2016. Single stool samples were collected from 1465 participants by clean stool cup. The questionnaire was prepared on the basis of demographic characteristics. The diagnosis was made on the basis of the direct wet mount, formalin-ether concentration, and Ziehl-Neelsen and trichrome stained slides. Out of the 1465 school children examined, six species of intestinal parasites were identified with an overall prevalence of 95 positive students (6.5%). Prevalence of protozoan infections (6.2%) was significantly higher than helminth infections (0.3%). The most common protozoan species were ( = 42, 2.9%) and ( = 31, 2.1%). Only two cases of and two cases of were detected. The prevalence of parasitic infections was higher in boys ( = 52, 7%) than girls ( = 41, 5.7%), but the difference was not significant. The parasitic infections were higher among the children whose parent's education was less than high school diploma ( = 0.000), and there was also a significant association between the parents' jobs and the intensity of parasitic infection. The prevalence of intestinal parasites, compared to the previous studies in this area, was significantly lower; that is mainly due to an increase in the quality of life and parents' education as well as the accessibility to health services. The most prevalent intestinal parasite was ; therefore, it is recommended that more emphasis is applied to controlling and preventing this parasitic infection by washing hands, particularly before each meal course.