Objectives Current strategies for controlling non-urogenital chlamydia and gonorrhoea are not uniform. It is assumed that present anorectal/oropharyngeal infections are coincidentally treated with urogenital infections. However, it is not clear whether this control strategy is effective. To inform current debate, we evaluated the anatomical site distribution of chlamydia and gonorrhoea by routine testing in men who have sex with men (hereafter men) and in high-risk women (prostitutes and swingers, hereafter women). Methods Between January 2010 and November 2012, all men (n=2436) and women (n=1321) attending our sexually transmitted infection clinic were routinely tested for anorectal, oropharyngeal and urogenital Chlamydia trachomatis and Neisseria gonorrhoeae. Data were collected on demographics and sexual behaviour. Results Overall chlamydia positivity was 10.4% (254/2436) in men and 7.0% (92/1321) in women, for gonorrhoea this was 6.3% (154/2436) and 3.1% (41/1321), respectively. Isolated non-urogenital infections amounted to 76% of all infections in men and for up to 59% of all infections in women. For combined urogenital and anorectal infections, this amounted to 14% for men and up to 54% for women. Conclusions Testing only for non-urogenital infections is insufficient, as it overlooks many infections. The use of coincidental treatment is therefore a suboptimal control strategy in high-risk groups for halting complications and transmission. There is an urgent need to optimise the testing guidelines for chlamydia and gonorrhoea at different anatomical sites.