Case-notes and laboratory data were retrospectively reviewed for influences of dual testing by Aptima Combo 2 (AC2) for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) on the diagnosis, management and prevalence estimation of gonorrhoea in the genitourinary (GU) medicine clinic and community. NG positives by AC2 were confirmed by Aptima Gonococcus assay. Unconfirmed positives were rare. Our study showed that in the GU medicine clinic, AC2 detected about 20% extra cases of NG beyond culture. For best standard of care, NG culture and microscopy are still required in some patients to ensure that treatment is rapid and appropriate. Compared to self-referral at the GU medicine clinic, community tests made a substantial contribution to the overall number of NG cases found (40 community versus 35 Macclesfield GU medicine clinic). The ratio of female to male NG cases found was significantly higher (P = 0.002) in the community (13 M, 27 F) than at the GU medicine clinic (25 M, 10 F). In the community, over 60% of NG infections occurred in chlamydia-negative patients. The overall prevalence of NG in the GU medicine clinic was 1.3%, the true prevalence being much lower at 0.9% on primary test. Prevalence in the community was 0.4%. Data from dual testing in the community can clarify NG prevalence beyond the existing KC60 (sexually transmitted infections) reports.