Anal sex is a common sexual behavior among women that increases their risk of acquiring rectal infection with Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC). We estimated the frequency and positivity of rectal CT and GC tests for women aged 15-60 years performed by a large US commercial laboratory between November 2012 and September 2015. We also estimated the frequency and positivity of pharyngeal and genital specimens also performed on the same date. Among women with a positive CT or GC result, we estimated the frequency and positivity of recommended repeat testing within 12 months. Of 5499 women who had rectal CT and GC tests, positivity was 10.8%. On the same date, approximately 80% also had genital CT tests, genital GC tests, and pharyngeal GC tests, while 40% had pharyngeal CT tests. Rectal CT or GC infection was associated with genital CT or GC infection, but 46.5% of rectal CT and GC infections would not have been identified with genital testing alone. Among women with a rectal CT or GC infection, only 20.0% had a recommended repeat rectal test. Of those who had a repeat test, 17.7% were positive. Testing women for rectal CT and GC was infrequent, but positive tests were often found in women with negative genital tests. Most women with positive rectal tests were not retested. Interventions are needed to increase extragenital CT and GC testing of at-risk women.