Introduction: Enterobiasis is one of the main intestinal infections worldwide. Objective: Determine the factors associated to Enterobius vermicularis infection in children from two native Ese’Eja communities in Madre de Dios, Peru. Methods: An analytical cross-sectional study was conducted in February-March 2014 of 77 children aged 1-11 years. Enterobiasis diagnosis was based on Graham's test. Clinical manifestations were evaluated by a physician, whereas associated factors were determined through a survey applied to the parents of the children studied. Use was made of descriptive and analytical statistical analysis, and crude and adjusted prevalence ratios with a CI of 95%. A p value of 0.05 was considered significant. Results: Enterobiasis prevalence was 32.47% (25). The associated factors (PR and CI 95%) in the bivariate analysis were onychophagia 2.1 (1.1-3.9), finger sucking 5.4 (2.1-2.7), long nails 7 (2.6-18.6), exchanging clothes 2.3 (1.1-3.7), changing underwear 3.3 (1.8-5.9), wearing shoes 7 (2.6-18.4), playing with earth 6.9 (1.7-27.3), playing with pets 6.4 (2.1-19.7), handwashing before eating 7.9 (3.6-17.1), handwashing after eating 1.9 (1.7-3.66), six or more people in the household 3.9 (1.9-7.9), feces disposal in open areas 3.3 (1.7-6.2) and a lower socioeconomic level 2.6 (1.3-5.4). Multivariate analysis did not find any association. Conclusions: Enterobiasis prevalence is high in the population studied, and the risk factors are similar to the local antecedents. It is urgent to develop health prevention and promotion programs about the topic to reduce this problem.