Background and Objectives: Chlamydia truchomatis can be directly transmitted by sexual or perinatal contact and indirectly transmitted by flies or fomites. Whether distinct epidemiologic forces among human populations or biologic characteristics of the organism are responsible for the different routes of transmission is uncertain. Study Design: To determine if ophthalmia neonatorum and trachoma are linked epidemiologically, 38 infants with ophthalmia and 277 children with trachoma were studied for evidence of C. truchomatis infection using culture, antigen and DNA detection tests. The study was performed in a trachoma endemic area of central Kenya. Results: Of infants with ophthalmia neonatorum, 8% to 9% had microbiologic evidence of ocular C. truchomatis infection. Of the children with trachoma, 31% had evidence of chlamydial infection. Ninety-two percent of the 59 identified strains causing trachoma belonged to the classic trachoma serovars (A, B, Ba and C). Neither of the two chlamydia1 strains recovered from infants with ophthalmia was a trachoma serovar. Mothers rarely (3%) had cervical C. trachomatis infection. Conclusion: This study does not support a major role for perinatally transmitted C. trachomatis infection in trachoma epidemiology.