Background Extremely high rates of diagnosis of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) have been recorded in remote communities across northern and central Australia. Re-testing at 3 months, after treatment administered, of CT or NG is recommended to detect repeat infections and prevent morbidity and ongoing transmission. Methods: Baseline CT and NG laboratory data (2009-2010) from 65 remote health services participating in a cluster randomised trial was used to calculate the proportion of individuals re-tested after an initial CT or NG diagnosis at <2 months (not recommended), 2-4 months (recommended) and 5-12 months and the proportion with repeat positivity on re-test. To assess if there were difference in re-testing and repeat positivity by age group and sex, t-tests were used. Results: There was a total of 2054 people diagnosed with CT and/or NG in the study period; 14.9% were re-tested at 2-4 months, 26.9% at 5-12 months, a total of 41.8% overall. Re-testing was higher in females than in males in both the 2-4-month (16.9% v. 11.5%, P<0.01) and 5-12-month (28.9% v. 23.5%, P≤0.01) periods. Women aged 25-29 years had a significantly higher level of re-testing 5-12 months post-diagnosis than females aged 16-19 years (39.8% v. 25.4%, P<0.01). There was a total of 858 people re-tested at 2-12 months and repeat positivity was 26.7%. There was higher repeat NG positivity than repeat CT positivity (28.8% v. 18.1%, P<0.01). Conclusions: Just under half the individuals diagnosed with CT or NG were re-tested at 2-12 months post-diagnosis; however, only 15% were re-tested in the recommended time period of 2-4 months. The higher NG repeat positivity compared with CT is important, as repeat NG infections have been associated with higher risk of pelvic inflammatory disease-related hospitalisation. Findings have implications for clinical practice in remote community settings and will inform ongoing sexual health quality improvement programs in remote community clinics.