Trends in the frequency of clinical encounters for pelvic inflammatory disease (PID) and epididymitis in Australian general practice were determined via a national representative study of general practice activity between 1998 and 2003. Information was derived from 502,100 general practice encounters that occurred during the study period. An estimated 59,200 encounters for PID and 54,200 encounters for epididymitis took place in Australian general practice each year. Despite increases in national notification rates for Chlamydia trachomatis, over the study period overall encounter rates did not change significantly for either condition, and a fall in encounter rates for PID of about 50% occurred among women aged 15-34 years (P=0.02). Only 0.3% of encounters for PID and 1.9% of those for epididymitis resulted in hospital referral. On a population level, trends in the incidence of chlamydia-related diseases do not necessarily parallel those of reported chlamydia rates.