Background Both anorectal Chlamydia trachomatis (CT) and Neisseria gonorrhoea (NG) can occur as a rectal-only infection or concurrently with simultaneous urogenital infection with the same pathogen. Characterising the target groups in which rectal-only infections occur may improve the efficacy of screening practices. Methods We analysed data from two Dutch outpatient sexually transmitted infection (STI) clinics between 2011 and 2012. We included all men who have sex with men (MSM) (n = 9549) and women (n = 11113), >= 18 years, who had been tested for anorectal and urogenital CT and/or NG (either as a result of reporting anal sex/symptoms or via routine universal testing). Factors associated with rectal-only CT and NG infections were assessed using univariable and multivariable logistic regression. Results In MSM, anorectal CT prevalence was 9.8% (693/7094), anorectal NG prevalence was 4.2% (397/9534). In women this was 9.5% overall (439/4597) and 0.9% (96/10972) respectively. Anorectal CT prevalence among women who were routinely universally tested was 10.4% (20/192), for selective testing this was 9.5% (419/4405) (p = 0.68). Anorectal NG infections were not detected among women who were routinely universally tested (p = 0.19). Among CT or NG positive MSM, rectal-only CT infections were found in 85.9%(595/693), for NG this was 85.6% (340/397) respectively. In positive women these figures were 22.1% (97/439) for CT and 20.8% (20/96) for NG, respectively. In MSM, independent factors associated with rectal-only CT were: being a sex worker (OR0.4, CI0.2-1.0), exclusively having sex with men (OR3.4, CI1.7-6.8), and absence of urogenital symptoms (OR0.2, CI0.2-0.4). In women, these factors were: older age (OR2.3, CI1.3-4.0) and non-Western nationality (OR1.8, CI1.0-3.5). Factors associated with rectal-only NG in MSM were: having been warned for STIs by an (ex) partner (OR2.9, CI1.1-7.5), oropharyngeal NG infection (OR2.4, CI1.0-5.3), and absence of urogenital symptoms (OR0.02, CI0.01-0.04), while in women no significant factors were identified. Conclusions The prevalence of anorectal CT and NG was substantial in MSM and prevalence of anorectal CT was also substantial in women. Anorectal infections occurred mostly as rectal-only infections in MSM and mostly concurrent with other infections in women. Given the lack of useful indicators for rectal-only infections, selective screening based on a priori patient characteristics will have low discriminatory power both in relation to MSM and women.