To investigate the association of condom use with chlamydia infection in men attending a large sexually transmitted infection (STI) clinic in Australia. Computerized records for all attendances between July 2002 and June 2003 were included and separate analyses were performed for men reporting male-to-male sexual contact (MSM) and for men reporting heterosexual contact only (non-MSM). Associations among age, condom use, and number of partners with chlamydia infection were assessed. Chlamydia was diagnosed at a rate of 8.6 cases per 100 consultations (95%CI: 7.1, 10.3) among MSM and at a rate of 6.8 cases per 100 consultations (95%CI: 5.9, 7.8) among non-MSM. Condom use was associated with a lower odds of rectal chlamydia but not urethral infection in MSM. Condom use was associated with lower odds of urethral chlamydia among non-MSM. The findings suggest that condoms do provide some protection against rectal chlamydia infection in MSM and chlamydial urethritis in non-MSM, but other factors may play an important role in the transmission of chlamydial urethritis in MSM.