Background Young women receiving family planning services are at risk for both unintended pregnancy and herpes simplex virus type 2 (HSV-2) infection. Methods We performed a secondary analysis using data from a previously published randomized controlled trial evaluating access to emergency contraception on reproductive health outcomes. Women aged 15 to 24 years were recruited from two Planned Parenthood clinics and two community health clinics in San Francisco. Demographic information and sexual history were obtained by interview. HSV-2 seropositivity was determined by fingerstick blood test. New pregnancies were measured by self-report, urine testing and medical chart review. Subjects were evaluated for incident HSV-2 infection and pregnancy at a 6-month follow-up appointment. Women who were pregnant or intending to become pregnant at enrolment were excluded. Results At enrolment 2,104 women were screened for HSV-2 and 170 (8.1%) were seropositive. Eighty-seven percent of initially seronegative women completed the study (n = 1,672) and 73 (4.4%) became HSV-2 seropositive. HSV-2 seroincidence was 7.8 cases per 100 person-years. One hundred and seventeen women (7%) became pregnant and 7 (6%) of these had a seroincident HSV-2 infection during the study. After adjustment for confounders, predictors of incident HSV-2 infection were African American race and having multiple partners in the last six months. Condom use at last sexual encounter was protective. Conclusion HSV-2 seroincidence and the unintended pregnancy rate in young women were high. Providers who counsel women on contraceptive services and sexually transmitted infection prevention could play an expanded role in counselling women about HSV-2 prevention given the potential sequelae in pregnancy. The potential benefit of targeted screening and future vaccination against HSV-2 needs to be assessed in this population.