Cell culture has traditionally been considered the most sensitive method for detecting Chlamydia trachomatis from clinical specimens, but depends upon the organisms being viable at the time of cell inoculation. Furthermore, cell culture is slow and labor intensive. Even when a special transport medium is used, there is a progressive loss of viability of C. trachomatis during transport. The detection of C. trachomatis by cell culture is more rapid when immunofluorescence is used to detect early antigen, but requires considerable experience to interpret. The Amplicor C. trachomatis system is a commercial polymerase chain reaction (PCR)-based assay combined with nucleic acid hybridization for the direct detection of C. trachomatis in urine and swabs of appropriate sites, with results available within 6 h. All specimens for C. trachomatis received by the Royal Perth Hospital Department of Microbiology during the period 1 July 1994 to 30 June 1995 that were suitable for culture and Amplicor PCR were tested by both methods (2029 specimens). Discordant results were obtained in nine cases and resolved by additional testing. Seventy-one specimens were confirmed as true positives, of these Amplicor PCR correctly detected 67 (sensitivity 94.4%) and culture correctly detected 62 (sensitivity 87.3%). The Amplicor PCR assay was found to be more sensitive and as specific as culture. It had the added advantages of ease of use, rapid availability of results, standardization and was more suited than culture to processing large number of specimens.