Background: Over the last decade, significant advances have occurred in the area of chlamydia diagnostics. The relative frequency of different testing methods employed in the diagnosis of Chlamydia trachomatis infection in New South Wales has not been previously reported. Methods: Testing methods-both laboratory method and specimen type-employed in the diagnosis of chlamydia cases notified in New South Wales between 1999 and 2002 were collated from Health Department records. Results: During a period of increasing notifications, the proportion of men diagnosed with C. trachomatis using nucleic acid tests (NATs) increased from 36% in 1999 to 90% in 2002. Among women, the proportion diagnosed using NATs increased from 42% in 1999 to 92% in 2002. Urine samples were consistently used in the diagnosis of two-thirds of the men, and one-third of the women. Conclusion: Between 1999 and 2002, a rapid shift towards NATs for genital C. trachomatis took place in New South Wales.