We undertook a systematic review to examine rectal Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) infections in women and men who have sex with men (MSM). English-language publications measuring rectal Ct or Ng prevalence using nucleic acid amplification tests were eligible. Searching multiple electronic databases, we identified 115 eligible reports published between January 2000 and November 2016. Overall, the prevalence of rectal Ct (9%) was higher than that of rectal Ng (4.7%). Rectal Ct prevalence was similar in MSM (9%) and women (9.2%), whereas rectal Ng prevalence was higher in MSM (6.1%) than in women (1.7%). Generally, rectal Ct prevalence was similar in sexually transmitted disease clinics (9.1%) and nonsexual health clinics (8.6%), whereas rectal Ng prevalence was somewhat lower in sexually transmitted disease clinics (4.5%) than in nonsexual health clinics (6%). These infections seem to be relatively common across a range of populations and clinical settings, highlighting the need for additional research on these preventable, treatable conditions.