Timely treatment of sexually transmitted infections can reduce complications and prevent onward transmission. Several audit standards exist in this area. We audited the timeliness of treatment of 538 episodes of chlamydia at 12 Scottish genitourinary medicine clinics against a national standard and against a local best practice target. Three clinics treated 95% of patients within two weeks and 10 clinics treated 95% of patients within four weeks. All clinics treated 60% of patients within four weeks. Overall, all clinics performed well against published standards, but less well against the best practice target.