To determine the prevalence of endoparasites and their association with diarrhea, a survey was conducted in the Southern Province of Zambia that used conventional and molecular techniques applied to stool and urine samples from school-age children (n = 93). Almost half of the stools (49.5%) were diarrhetic. The overall prevalence of Endolimax nana, Schistosoma haematobium, Blastocystis hominis, Giardia lamblia, Cryptosporidium parvum, Encephalitozoon intestinalis, and Strongyloides stercoralis was 64.3, 59.1, 53.8, 19.4, 8.6, 8.6, and 1.1%, respectively. Only the associations between infection with B. hominis and E. nana with diarrhea were statistically significant. Although B. hominis and E. nana are considered to be nonpathogenic organisms, this study demonstrated that they can be associated with diarrhea in children when they occur at high prevalence and intensity. This survey supports the recent evidence that B. hominis and E. nana infections are associated with deficient sanitation and low hygiene standards and can contribute to diarrhea in children in developing countries.