OBJECTIVES: Chlamydia trachomatis infections, in the context of extreme poverty, may trigger trachoma. Because the levels of C. trachomatis eye infections in Mexico are unknown, this study sought to determine if C. trachomatis was present in the conjunctiva of children living in three poor, rural areas of the country. METHODS: Clinical diagnosis of conjunctival follicles in children was conducted during the 2004 visual acuity assessment campaigns in rural areas of the states of Chiapas, Oaxaca, and Zacatecas. C. trachomatis detection was carried out by sampling the children with follicles and examining the specimens after Giemsa or microimmunofluorescence (MIF) staining. RESULTS: A total of 941 children from 6 to 12 years of age were examined in 2004. Of the 484 in Chiapas, 30% were found to have follicles; of the 181 in Zacatecas, 22%; and of the 276 in Oaxaca, 42%. C. trachomatis was detected at levels ranging between 2% and 5%; positive by Giemsa in 4.5% of the children with follicles, and by MIF in 15.5%. CONCLUSIONS: Considering that the chlamydiae sampling procedures and detection methods used in this study were not the most sensitive, the results underestimate the chlamydial eye infections and represent a conservative assessment of a potential risk for preventable visual impairment. Because C. trachomatis was detected here at levels similar to those reported for low-endemic trachoma areas, health authorities should be prepared to implement appropriate measures should it be confirmed that the visual health of Mexico’s children is at risk.