This paper reports rates of retesting and repeat positivity 6 weeks to 6 months following diagnosis of chlamydia or gonorrhoea between July 2012 and July 2015 in Wellington primary care and sexual health clinics. Of all 6530 cases, 1919 (29%) were retested between 6 weeks and 6 months; 347 (18%) of those retested returned positive results. In logistic regression analysis adjusted for potential confounders (age, gender, ethnicity and socioeconomic deprivation), factors associated with significantly lower odds of retesting included male gender (OR 0.4; 95% CI, 0.34 to 0.48, reference female), New Zealand Māori (OR 0.72; 95% CI, 0.61 to 0.85, reference European) and Pacific ethnicities (OR 0.49; 95% CI, 0.39 to 0.62, reference European). Factors associated with significantly higher odds of repeat positivity when retested included male gender (OR 2.0; 95% CI, 1.14 to 2.82), younger age (15–19 years, OR 1.78; 95% CI, 1.32 to 2.41, reference 20–24 years), chlamydia/gonorrhoea co-infection at the index event (OR 2.39; 95% CI, 1.32 to 4.35, reference chlamydia only), New Zealand Māori (OR 1.6, 1.18 to 2.17, reference European) and Pacific ethnicities (OR 1.88; 95% CI, 1.22 to 2.9, reference European).