Objective: To evaluate the prevalence and risk factors of intestinal parasitic infections in the urban and rural areas of Shushtar County, southwest Iran. Methods: A total of 1 008 fecal samples were analyzed by direct smear examination, formalin-ether concentration, and Ziehl-Neelsen and trichrome staining; furthermore, PCR was used to distinguish Trichostrongylus and hookworm species based on 28S rRNA gene. Results: Totally, 16.0% cases tested positive, either with a pathogenic or a non-pathogenic parasite. Protozoa were detected in 14.0%, helminths in 1.0%, protozoa and helminth co-infections were detected in 0.3%, and co-infections of two protozoa were detected in 0.7% of cases. The most common protozoa and helminths were Giardia duodenalis (7.7%) and Trichostrongylus spp. (0.5%), respectively. Among five microscopy Trichostrongylus positive cases, Trichostrongylus culbriformis was successfully identified in three isolates by sequencing. In the rural areas, the prevalence of parasitic infection was higher (9.8%) than that in the urban areas (6.2%). A significant association was found between educational level, type of drinking water, animals contact, hand-washing, and clinical symptoms. Conclusions: This study indicates that intestinal parasitic infections remain as a public health priority in Shushtar County. It seems that drinking water and environmental sanitation are the main risk factors of parasitic infections in rural areas.