Sexually transmitted rectal infections with Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) have been well documented in men who have sex with men (MSM). Few studies have described infections in women who engage in anal intercourse. We performed testing for rectal infections in women who reported ano-receptive intercourse at the Miami Dade Health Department Sexually Transmitted Diseases (STD) clinic and report the prevalence and characteristics of women with rectal CT or GC infections. Our results revealed a prevalence of 17.5% for rectal chlamydia and 13.4% for rectal gonorrhoea. Urine-based screening alone would have missed 6% of rectal chlamydia infections and 35% of rectal gonorrhoea infections. Anal symptoms were reported in 12.5% of women with rectal chlamydia infections. The only associated factor identified was an age less than 28 years. We conclude that rectal screening for CT and GC should be included in STD prevention strategies, especially in the younger population.