BackgroundChlamydia trachomatis is the most prevalent bacterial sexually transmitted infection (STI) in the world. Approximately 80% of infected women are asymptomatic, although this infection can lead to serious complications in the female reproductive tract. Few data on Chlamydia infection are available in rural Amazonian communities.ObjectivesTo evaluate the prevalence of sexual C. trachomatis infection in women from Marajó Archipelago communities in the Amazon region of Brazil and to identify associated factors and genotypes.MethodsWe utilized amplification of the ompA gene by nested PCR. Positive samples were genotyped by sequencing. Study participants completed a questionnaire on social, epidemiological, and reproductive health variables. A Poisson regression was used to evaluate the degree of association of these variables with the infection.ResultsThe sexual infection by C. trachomatis was observed in 4% (16/393) of the subjects, and was more often found in women aged ≤25 (14.3%; 95% CI = 2.83–35.47; p <0.001), and in women with a household income of less than one Brazilian monthly minimum wage (5.2%; 95% CI = 1.33–11.37; p = 0.014). The ompA gene was sequenced in 13 samples, revealing F genotypes (38.4%, n = 5), D (23%, n = 3), E (15.3%, n = 2), Ia (7.6%, N = 1), J (7.6%, n = 1) and B (7.6%, n = 1).ConclusionsWe recorded a high prevalence of sexual infection by C. trachomatis in young and poor women from the interior of the Brazilian Amazon. This high prevalence and the frequencies of the main genotypes were similar to those found in major Brazilian urban centers. Our results reinforce the importance of the screening of this neglected infection, and the prevention of later sequelae in young women from rural and urban areas of Brazil.