Objective: To estimate completion rate and acceptability of home screening for sexually transmitted infections (STIs) compared with clinic-based screening in a prospective cohort study. Methods: The first 462 women enrolled in the Contraceptive Choice Project were screened at the 12-month follow-up for Chlamydia trachomatis and Neisseria gonorrhoeae using strand displacement analysis of self-collected vaginal swabs. In a telephone interview, participants were given a choice of no-cost screening with swabs mailed to the participant's home (home-based) or screening that was available at area family planning clinics without an appointment (clinic-based). The clinic-based group also included women who elected to screen with their regular provider according to the clinician's normal practice. We analyzed the rates of screening, including patient preference and the proportion of completed tests by testing method. Results: Women were more likely to choose to screen for STIs at home than at a clinic or with their own medical provider (75.7% compared with 16.1% compared with 8.2%, P<.001). Women choosing clinic testing were more likely to be African American than those choosing home testing. African-American women constituted 42% of the clinic group compared with 28% of the home group (relative risk [RR] 1.63, 95% confidence interval [CI] 1.14-2.31). The groups did not differ in other demographic characteristics, STI risk factors, or access to health care. Overall, 228 women (56.6%) completed screening. Women who chose home-based testing were more likely to complete a test compared with all clinic-based testers (64.6% compared with 31.6%, RR 2.04, 95% CI 1.51-2.76). Conclusion: Women overwhelmingly preferred to screen for STIs at home. Future interventions to increase screening rates in young women should consider alternative screening strategies such as home-based or patient-controlled testing.