We have examined the relationship between Chlamydia trachomatis found in clinical samples in which the cryptic plasmid was absent and known serovars of C. trachomatis. PCR and RNase protection assays were used to compare 12 C. trachomatis serovars and a plasmidless L2 serovar strain with the reactivity of clinical specimens taken from patients with pelvic inflammatory disease (PID) containing the C. trachomatis 16S rRNA gene and 16S rRNA but lacking plasmid DNA. Serovars D, E, H and I were unreactive in either or both of the PCR and RNase protection assays. The plasmidless L2 strain had reactivities indistinguishable from the nucleic acids found in the PID clinical specimens. Serovar D, the plasmidless L2 strain, and nucleic acids from two of the PID specimens were further compared by amplifying, cloning and sequencing the 16S rRNA genes detected in these samples. The sequences of the 16S rRNA genes detected in the PID clinical samples and the 16S rRNA gene of the plasmidless C. trachomatis variant were indistinguishable from previously reported sequences of the C. trachomatis 16S rRNA. Serovar D showed five base changes over the same region. We conclude that although these clinical samples lack the C. trachomatis cryptic plasmid, they do contain C. trachomatis nucleic acid.