The aim of this study was to assess the presence of inhibitors in urine specimens causing false-negative results in a commercial Chlamydia trachomatis gap-filling ligase chain reaction (Gap-LCR) assay. On testing of urine samples by the Gap-LCR assay and urethral swab specimens by cell culture, 73 (19%) Chlamydia trachomatis positive subjects were detected among 382 men attending a clinic for sexually transmitted diseases. In 56 subjects, the agent was detected in both the urine and the urethral samples, while 309 subjects were negative in both tests. In seven subjects urine samples were Gap-LCR positive (confirmed by a different Gap-LCR assay), but the corresponding urethral swab samples were cell culture-negative. In another ten subjects the urethral swab samples were cell culture positive, but their urine samples were Gap-LCR negative. Subsequent re-analysis of the urine samples including the addition of external Chlamydia trachomatis DNA indicated full or partial inhibition in nine of the cell culture-positive Gap-LCR negative subjects. When urine preparations were freeze-thawed and diluted prior to testing, Chlamydia trachomatis was detected in six of the ten initially Gap-LCR-negative samples. Gap-LCR inhibitors were present in at least nine (12%) of the 73 urine preparations from the Chlamydia trachomatis positive individuals. Identification of samples containing Gap-LCR inhibitors and subsequent processing to reduce the inhibition increased the sensitivity of the test from 86% to 95%.