Objective: To compare prevalences of intestinal helminths and waterborne protozoa in indigenous and settler populations in a remote area of Peru. These populations live in adjacent but segregated small urban villages. Methods: Stool samples were collected from representative members of these two populations and analysed for geohelminths and protozoa. Results: The risk of soil-transmitted helminths is significantly higher in the settler than the indigenous population in the same isolated region of Peru (OR 5.18; 95% CI 3.44-7.81; P < 0.001). In contrast, the rates of protozoa presence were similar in both populations (OR 1.28; 95% CI 0.77-2.14; P = 0.336). Conclusions: Potential explanations for unexpected finding of a lower prevalence of helminths in indigenous relative to the settler population could include housing design in flood - prone areas and the use of local medicinal plants that possibly have antihelmintic properties. © 2013 Blackwell Publishing Ltd.