Disclosed are methods and compositions for conducting assays of samples utilizing polymerase chain reactions (“PCRs”) in the detection of serotypes of Chlamydia trachomatis capable of causing lymphogranuloma venereum (“LGV”). These serotypes are in the L group of Chlamydia trachomatis, and include the L I, L II, and L III serotypes. These assays take advantage of a deletion occurring in the cytotoxin gene locus specific to the L I, L II, and L III serotypes. The genome of each of these three serotypes contains the nucleotide sequence of SEQ ID NO:1 and the nucleotide sequence of SEQ ID NO:2, wherein the nucleotide at the 3′ end of SEQ ID NO:1 and the nucleotide at the 5′ end of SEQ ID NO:2 are contiguous, and wherein the deletion point of the cytotoxin gene locus is located between these two nucleotides. Each of these assays employs a first primer having a nucleotide sequence flanking one side of the deletion point and a second primer having a nucleotide sequence flanking the other side of the deletion point, wherein the first primer and the second primer are capable of hybridizing respectively to the plus strand and the minus strand of the genome of Chlamydia trachomatis during the PCR. Synthesis during the PCR of a sequence-specific amplicon containing this deletion point indicates that the sample contains nucleic acid specific to an LGV-causing serotype of Chlamydia trachomatis. The amplicon can be detected during real-time PCR using a labeled oligonucleotide as a probe, or after end-point PCR by gel electrophoresis.