We performed a cross-sectional parasitological survey to assess the prevalence of protozoa and helminth infection among 275 school-age children (SAC) living in rural and peri-urban areas located in different ecological zones of the Department of La Paz, Bolivia. Public health activities for the control of STH, based on the biannual administration of mebendazole to preschool and school children are implemented at national level since 1986. We found an overall prevalence of 82.2% for intestinal parasites, including protozoa (80%) and helminths (23.3%). Blastocystis and Entamoeba coli were the most prevalent protozoa (found in 44% and 20.7% of the SAC enrolled); as for helminths, Ascaris lumbricoides and Hymenolepis nana were diagnosed in 14.5% and 3.3% of the children, respectively, followed by Trichuris trichiura 1.4%, Enterobius vermicularis 1.4%, Strongyloides stercoralis 0.7% and hookworms 0.7%. Molecular characterization of Blastocystis positive samples evidenced three different subtypes (ST1, ST2, ST3) highlighting the risk of transmission also from animal reservoir. We found a significant difference in the distribution of intestinal parasitic infection (IPIs) by ecological zone (44/74. 59% in Andean highlands, 94/170, 88% in tropical lowlands and 88/94, 94% in the Yungas, p < 0.001). Access to potable water (OR 0.1 95%CI 0.02-0.5, p = 0.004) and the habit of boiling drinking water (OR 0.3, 95% CI 0.2-0.7, p = 0.004) showed an independent association with a lower risk of all IPIs and STHs, respectively. The very low prevalence of STH infections of moderate heavy intensity demonstrate that periodical deworming has been successful in reducing the morbidity due to these parasites, however the high prevalence of protozoa demonstrate that sanitation is still problematic and there is a relevant contamination of the environment with human faeces. Significant efforts are still needed to reduce IPIs transmission and to improve health and sanitation in this area.