BACKGROUND: Men who have sex with men (MSM) are at increased risk for extra-genital sexually transmitted infections (STIs). Without extra-genital screening, many chlamydia and gonorrhea infections would be missed among MSM. Yet, many barriers exist to extra-genital testing, and, in particular, to rectal collection. Self-collection increases screening and detection of asymptomatic chlamydia and gonorrhea among at-risk MSM and transgender women. This feasibility study assessed use of rectal self-collection and its acceptance among patients and primary care providers (PCPs) at a large, general practice community health center. The primary objective of this project was to assess the feasibility of including rectal self-collection as part of an implementation study looking to embed an STI care program in a safety-net primary care setting that would shift routine screening tasks to non-provider clinical team members such as medical assistants and nurses. METHODS: Three PCPs identified and offered rectal self-collection to their MSM and transgender female patients who were due for routine or risk-based STI screening. For those patients who elected to participate in the study, the PCP's medical assistant (MA) reviewed the self-collection instructions with them as part of their routine preventive care duties, and patients collected their own sample. Patients and PCPs completed brief cross-sectional surveys assessing the self-collection process. RESULTS: Of 1191 patients with sexual orientation and gender identity (SOGI) data on file who were seen for a medical visit by one of the three PCPs, 87 (7.3%) identified as MSM or transgender female. Seventy-five were due for rectal screening, of whom 33 (44%) were offered and completed rectal self-collection. Survey results indicated that self-collection was acceptable to and preferred over clinician-collection by both PCPs and patients. CONCLUSIONS: This study demonstrated that rectal self-collection is feasible as part of STI screening in a high-volume primary care setting, and can be administered as part of the clinical tasks that MAs routinely conduct. The overall acceptance by both PCPs and patients will allow the inclusion of rectal self-collection in an implementation study looking to increase STI screening at a large community health center by facilitating MA-led collection during medical provider visits and by establishing standalone nurse-led STI visits.