High prevalence of chlamydia in the USA persists despite efforts to annually screen women under the age of 26. Tailoring sexually transmitted infection (STI) services to client preferences may strengthen existing programmes. We report women's preferences for STI services from a family planning clinic in New York City serving low-income women. Seventy-eight percent (995/1275) of eligible women participated, with a mean age of 26 (SD±7). Ninety-one percent self-identified as Latina. Nineteen percent reported a past STI. Women preferred self-collection (65%) for testing to a speculum exam (20%); 15% had no preference. Women with a previous STI were more likely to prefer a pelvic exam to women with no previous STI (50% versus 32%, P < 0.01). Nearly all women (94%) preferred informing a sex partner about a positive STI test themselves, but 88% were willing to bring expedited partner therapy to a partner. Women were more likely to prefer third party partner notification if their last partner was casual rather than a main partner (14% versus 3%, respectively, P < 0.01). Forty-four percent of participants worried about physical violence after partner notification. Self-collecting specimens for screening was widely acceptable. Partner notification strategies should be based on understanding partnership status, including fears of violence.