Objective To investigate the current prevalence of human intestinal protozoal infections in Tibet Autonomous Region, so as to provide the scientific basis for the development of the future control strategy. Methods The study sites were sampled using a stratified cluster random sampling method in different ecological zones and different geographical locations of Tibet Autonomous Region in 2015. Fecal samples were collected from the permanent residents at ages of 3 years and older for the detection of intestinal protozoa cysts and trophozoites. The region-, gender-, age-, occupation- and education level-specific prevalence of human intestinal protozoal infections was estimated and compared. Results A total of 70 study sites were sampled from 23 counties (districts) in 3 ecological zones of Tibet Autonomous Region in 2015. Among 17 939 subjects surveyed, there were 1 117 residents infected with intestinal protozoa, with a prevalence of 6.23%. There were 9 species of intestinal protozoa identified, and Entamoeba coli (3.59%), Giardia lamblia (0.74%) and Blastocystis hominis (0.72%) were found to have a high in- fection rate. The prevalence of human intestinal protozoal infections was 7.20%, 6.39% and 4.48% in the southern, eastern and northern Tibetan ecological zones, respectively. Among the 23 counties (districts), the highest human prevalence was seen in Baingoin (13.56%) and Amdo counties (12.77%), and there were significant differences in the prevalence of human intestinal pro- tozoal infections among the three ecological zones (χ2 = 33.909, P < 0.01) and 23 counties (districts) (χ2 = 580.511, P < 0.01). There was no gender-specific prevalence of human intestinal protozoal infections (men, 6.08%; women, 6.35%; χ2 = 0.542, P > 0.05); however, there was age-specific human prevalence (χ2 = 44.377, P < 0.01), and a higher prevalence was seen in residents at ages of 60－69 years (8.51%) and 50－59 years (7.67%). In addition, there were occupation- (χ₂ = 37.568, P < 0.01) and education level-specific prevalence rates of human intestinal protozoal infections (χ2 = 14.659, P < 0.01), and a higher prevalence was seen in farmers (7.17%) and herdsmen (5.28%), and in residents with a primary school education (6.62% and illiterate resi- dents (6.33%). Conclusions The prevalence of human intestinal protozoal infections remains high in Tibet Autonomous Region. The health education pertaining to intestinal parasitic disease control requires to be intensified among farmers and herds- men in rural areas.