Achieving satisfactory retention in online HIV prevention trials typically has proven difficult, particularly over extended timeframes. The overall aim of this study was to assess factors associated with retention in the Men's INTernet Study II (MINTS-II), a randomized controlled trial of a sexual risk reduction intervention for men who have sex with men. Participants were recruited via e-mails and banner advertisements in December, 2007 to participate in the MINTS-II Sexpulse intervention and followed over a 12-month period. Retention across the treatment and control arms was 85.2% at 12 months. Factors associated with higher retention included: randomization to the control arm, previous participation in a study by the research team, e-mail and telephone reminders to complete a survey once it was available online, and fewer e-mail contacts between surveys. The results provide evidence that achieving satisfactory retention is possible in online HIV prevention trials, and suggest best practices for maximizing retention.