We determined the serovar distribution and genetic variability of the omp1 gene of C. trachomatis in nasopharyngeal aspirates from consecutive infants with pneumonia. C. trachomatis was detected by PCR in 17/94 (18.1%) specimens. Serovar E (47.1%) was the most frequent, followed by serovars F (17.6%), Ja (17.6%), D (11.8%), and G (5.9%). Nucleotide sequence analysis showed polymorphism of Omp1.