BACKGROUND: High prevalence of asymptomatic rectal chlamydia and gonorrhea (CT/NG) among women is increasingly recognized. Screening is controversial due to lack of natural history data. Barriers to screening may include reluctance to discuss anal sex and collect rectal samples. This study describes the prevalence of sexual contact exposing adolescent and young adult (AYA) women to extragenital STIs and acceptability of self- and clinician-collection of rectal samples, preference for self- versus clinician-collected rectal samples and preference for home or doctor’s office for sample collection. METHODS: Participants were recruited from a primary care office and completed structured interviews assessing types of sexual contact and attitudes about rectal sampling. Differences were tested using chi-square and two-sided Fisher’s exact test. RESULTS: Of 110 cisgender women (aged 14-22 years) enrolled, the average age was 18.4 years (SD 1.7); 83% reported a history of extragenital contact; 22% reported history of receptive anal intercourse. A majority of participants reported self- and clinician-collected rectal samples to be acceptable (86% and 73%, respectively), with preferences for self-collection (71%) over clinician-collection (29%, p < 0.001) and collection at the doctor’s office (85%) over home (15%, p < 0.001). CONCLUSIONS: AYA women engage in behaviors that increase risk for rectal STI. Self- and clinician-collected rectal samples were acceptable. A majority of AYA women preferred to collect rectal samples in the doctor’s office rather than at home. This may reduce adolescents’ access to direct-to-consumer STI services. Offering in-clinic, self-collected rectal samples may improve uptake of rectal STI screening in adolescent females.