Aims To describe the current burden and trends of sexually transmitted infections (STIs) in New Zealand (NZ) since 1999, as reported by current surveillance methods. Methods Clinic rates were calculated by dividing the number of diagnoses by the total number of clinic visits. Laboratory rates were calculated using the NZ Census 2001 population data for the Auckland, Waikato, and Bay of Plenty regions. Results In 2003, chlamydia was the most commonly diagnosed STI in sexual health (SHCs) and family planning clinics (FPCs), followed by genital warts. Laboratory surveillance reported a chlamydia rate of 653.0 per 100,000 population and a gonorrhoea rate of 90.2 per 100,000 population. The highest rates of chlamydia and gonorrhoea were in the 15 to 19 years age group. From 2002 to 2003, both chlamydia and gonorrhoea cases have increased by 14.0% in SHCs. In FPCs, chlamydia increased by 25.9% and gonorrhoea increased by 11.4%. Since 2002, numbers of chlamydia and gonorrhoea cases have increased by 14.0% in SHCs and by 25.9% and 11.4%, respectively, in FPCs. Maori and Pacific Peoples continue to be disproportionately affected by STIs. Conclusions Current national surveillance methods are unrepresentative of the NZ population and do not provide accurate estimates of the population burden of STIs. Expansion of laboratory surveillance (to accurately reflect all areas of NZ) is needed and is currently under active consideration.