INTRODUCTION: Diagnosis of Chlamydia trachomatis infection in newborns is difficult; however, this diagnosis is performed by cell culture or by detection of IgM antibodies against C. trachomatis. Detection of C. trachomatis DNA in peripheral blood leukocytes using polymer chain reaction (PCR) may be a better tool for the diagnosis of infection by this pathogen. MATERIAL AND METHODS: A total of 44 premature newborns, all weighing less than 2500 g, were included in the study. A blood sample and nasopharyngeal lavages were obtained from each newborn. Leukocyte DNA was obtained by phenol-chloroform extraction technique. Detection of C. trachomatis was performed by amplifying the ompA gene using the PCR endpoint. Cell culture tests and the detection of IgM antibodies against C. trachomatis by microimmunofluorescence assay were also performed. RESULTS: Twenty newborns were PCR-positive (45.5%), with this test being significantly associated with the presence of pneumonia (RR = 2.28; 95% CI: 1.01 to 5.17; P = .035). The cell culture of nasopharyngeal lavage was positive in only 7 samples and no significant association was observed with any clinical or laboratory data. The titer of IgM antibodies against C. trachomatis associated with PCR-positive was 1:32 (RR = 2.74; 95% CI: 1.21 to 6.23; P = .008), however this titer was not associated with the presence of pneumonia. CONCLUSION: DNA detection in peripheral blood leukocytes could be useful for diagnosis of C. trachomatis infection.