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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, Graphic abstractUnlabelled Image, Highlights • In the Department of La Paz, the current overall STH among school-age children prevalence is high (17.1%), with a patchy distribution throughout the region. • The prevalence of STH infections of moderate and heavy intensity shows that the morbidity due to these parasites has not been eliminated yet. • The preventive chemotherapy coverage should be significantly improved in all the at-risk populations, and strategy of PC delivery should be tailored to local conditions. • Updated epidemiological information is crucial to inform policy for STH control. • Significant efforts are still needed to reduce transmission and to improve health and sanitation in this area. Interventions should be inspired by the WASH principles, endorsed by the WHO.