Background: In Australia, chlamydia is the most commonly notifiable infection and over the past ten years chlamydia and gonorrhoea notification rates have increased. Aboriginal compared with non-Aboriginal Australians have the highest notifications rates of chlamydia and gonorrhoea. Regular testing of young people for chlamydia and gonorrhoea is a key prevention strategy to identify asymptomatic infections early, provide treatment and safe sex education. This study evaluated if a sexual health quality improvement program (QIP) known as SHIMMER could increase chlamydia and gonorrhoea testing among young people attending four Aboriginal primary health care services in regional areas of New South Wales, Australia. Methods: We calculated the proportion of 15-29 year olds tested and tested positivity for chlamydia and gonorrhoea in a 12-month before period (March 2010-February 2011) compared with a 12-month QIP period (March 2012-February 2013). Logistic regression was used to assess the difference in the proportion tested for chlamydia and gonorrhoea between study periods by gender, age group, Aboriginal status and Aboriginal primary health service. Odds ratios (OR) and their 95% confidence intervals (CIs) were calculated with significance at p<0.05. Results: In the before period, 9% of the 1881 individuals were tested for chlamydia, compared to 22% of the 2259 individuals in the QIP period (OR): 1.43, 95 % CI: 1.22-1.67). From the before period to the QIP period, increases were observed in females (13 % to 25%, OR: 1.32, 95 % CI: 1.10-1.59) and males (3 % to 17%, OR: 1.85, 95 % CI: 1.36-2.52). The highest testing rate in the QIP period was in 15-19 year old females (16 % to 29%, OR: 1.02, 95 % CI: 0.75-1.37), yet the greatest increase was in 20-24 year olds males (3 % to 19%, OR: 1.65, 95 % CI: 1.01-2.69). Similar increases were seen in gonorrhoea testing. Overall, there were 70 (11%) chlamydia diagnoses, increasing from 24 in the before to 46 in the QIP period. Overall, 4 (0.7%) gonorrhoea tests were positive. Conclusions: The QIP used in SHIMMER almost tripled chlamydia and gonorrhoea testing in young people and found more than twice as many chlamydia infections. The QIP could be used by other primary health care centres to increase testing among young people.