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Background: Pathogenic intestinal protozoa are considered as a serious public health problem in developing countries. This study aimed to elucidate the overall prevalence and spatial distribution of three common human pathogenic intestinal protozoan infections in Iran. Methods: Six English and Persian databases were explored for published papers on the prevalence of Entamoeba histolytica/dispar, Giardia lamblia, and Cryptosporidium spp. in the general population of Iran from 2000 to 2015. All eligible data were collected using a pre-designed data extraction form, and the overall prevalence was estimated using a random-effects meta-analysis model. We used ArcMap for mapping the prevalence of the studied protozoa and clustering analysis. Results: Altogether, 118 eligible papers from 24 provinces of Iran were included and analyzed. The weighted prevalence of E. histolytica/dispar, G. lamblia, and Cryptosporidium spp. infection among Iranian general population were calculated 1.3% (95% CI 1.1-1.5%), 10.6% (95% CI 9.6-11.5%) and 2% (95% CI 1.5-2.5%), respectively. Conclusion: Our findings indicated human intestinal protozoan infections caused by E. histolytica/dispar, G. lamblia, and Cryptosporidium spp. have still public health importance in some parts of Iran.