The aim of this study was to investigate the characteristics of patients co-infected with Chlamydia trachomatis and Neisseria gonorrhoea. A retrospective case-control study was performed, which included 399 co-infected patients seen at a sexually transmitted infection clinic in Copenhagen, Denmark. Case-control groups included 300 patients who tested positive only for N. gonorrhoea, 300 who tested positive only for C. trachomatis, and 300 who tested negative for both N. gonorrhoea and C. trachomatis in the same study period. For men, non-Danish origin (odds ratio (OR) 2.3, 95% confidence interval (Cl) 1.34–4.12), previous sexually transmitted infections with C. trachomatis (OR 3.3, 95% CI 1.94–5.92) and N. gonorrhoea (OR 10.6, 95% CI 6.36-17.76), and higher number of sex partners (OR 1.7, 95% Cl 1.40-2.28) were significantly associated with diagnosis of co-infection. For women, previous sexually transmitted infections with C. trachomatis (OR 6.7, 95% CI 3.89-11.78) and N. gonorrhoea (OR 10.4, 95% CI 4.99-21.71), and higher number of sex partners (OR 1.8, 95% CI 1.28-2.56) were significantly associated with a diagnosis of co-infection, whereas being of non-Danish origin was, in some cases, a protective factor (OR 0.3, 95% CI 0.17-0.69). Furthermore, this study demonstrated sex-associated characteristics that should raise concern about coinfection, including: for men, being of non-Danish origin, men who have sex with men status, and higher age, and, for women, young age, in particular, and previous sexually transmitted infections.