A significant impact of intestinal parasitic infections on public health has mostly been neglected. Parasitic infections are one of risk factors for malnutrition in children. In this study, a large-scale screening of intestinal parasitic infections among children in 16 schools in 6 regions of Thailand was performed. In addition, we compared sensitivity of methods currently employed for detection of intestinal parasitic infection. Fecal samples collected from 1,909 students were examined for intestinal parasites by simple smear, formalin-ethyl acetate concentration (FECT), and Locke-egg-serum (LES) medium culture methods. Seven hundred and thirteen samples were infected with at least one intestinal parasite. The highest prevalence (82.8%) was found in Kanchanaburi Province, western Thailand. Blastocystis spp was the most common (32.8%) parasite, followed by Giardia duodenalis (4.2%), Ascaris lumbricoides (3.6%), hookworms (1.6%), Entamoeba histolytica (0.7%), Trichuris trichiura (0.5%), Enterobius vermicularis (0.5%), Strongyloides stercoralis (0.4%), minute intestinal flukes (0.2%), and Taenia spp (0.1%). Mixed parasitic infections were found in 121 students. In a comparative study, we found that FECT was more sensitive (74.0%) than simple smear (55.0%) method for detecting helminths. However, sensitivity of these two methods is not significantly different for protozoan detection (31.2% by simple smear and 33.5% by FECT). LES culture technique was the most sensitive method (77.5%) for detecting Blastocystis spp. Our results indicate a high prevalence of intestinal parasite infection among Thai students. More sensitive methods should be developed for a large-scale screening of intestinal protozoan infection.