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Stool samples from 122 children living in an urban slum (n= 72) and rural (n= 50) areas were analyzed using multi-parallel real-time quantitative PCR to determine intestinal prevalence parasites from two communities in Colombia. Findings indicated a prevalence of 86.1% Blastocystis spp., 62.5% Giardia intestinalis, 19.4% Cryptosporidium spp., 19.4% Ascaris lumbricoides, and 5.6% Trichuris trichiura in an urban slum; and 76% Blastocystis spp., 68% G. intestinalis, 20% Entamoeba histolytica, 50% A. lumbricoides, 46% T. trichiura, and 2% Strongyloides stercoralis in rural areas. Polyparasitism was higher in rural (58%) than urban (25%) areas (P= 0.001). Trichuris trichiura burden was higher in the rural area (P= 0.002). Over 40% of helminthic infections in rural areas had a heavy parasite burden by WHO classification. Over half of urban and rural children were infected with G. intestinalis and Blastocystis spp. Our …