Culture on McCoy cell monolayers has been accepted as the reference method for the detection of Chlamydia trachomatis. Recent studies have shown that polymerase chain reaction (PCR)/nucleic acid hybridization based methods have increased sensitivity over culture while still retaining specificity. In situations where organism viability is of concern, due to factors such as transportation delays, culture is inappropriate. Regional laboratories therefore have not been able to utilize the reference method and have been forced to use less reliable methods. The aims of our study were to assess the feasibility of performing PCR to diagnose infections due to C. trachomatis in a regional laboratory using a new commercial kit--Amplicor (Roche Molecular Systems, Branchburg, NJ) and to compare the current enzyme-immunoassay (EIA) based-methods used in our laboratory (VIDAS [bioMerieux Vitek, Hazelwood MO] and IDEIA [Novo Nordisk Diagnostics, Cambridge, UK]) against PCR. Thirteen positive Amplicor specimens were found in 267 urine specimens collected from asymptomatic adolescent males and females. All 13 were confirmed positive using major outer membrane protein gene PCR (MOMP). VIDAS and IDEIA showed 100% correlation to each other but only detected 5/13 positives. Of 140 consecutive patients attending the regional sexual health clinic, 13 were Amplicor positive, 11/13 MOMP positive and 10/13 positive by VIDAS. Five of 254 patients attending the hospital antenatal clinic were positive by Amplicor, all being confirmed by MOMP. No PCR inhibition was detected in a random sample of 100 varied negative Amplicor tests using a modification of the Amplicor kit. No contamination was experienced. The Amplicor kit was shown to be suitable for use in the routine clinical laboratory with minimal disruption to workflow. For regional laboratories this kit should provide more accurate results than EIA based methods, particularly in the detection of asymptomatic persons.