Interventions to assist reproductive health decision-making in populations affected by sickle cell disease (SCD) or trait (SCT) lack proven efficacy over time. Our aim was to compare effects of CHOICES, a Web-based multimedia education program on implementing informed reproductive plans, and usual care education (e-Book) on reproductive knowledge, intention, and behavior over 24 months. We randomized 234 participants with SCD (n = 138) or SCT (n = 96) (age 18-35 years, 35 % male, 94 % African American) to CHOICES and e-Book groups. Participants completed a sickle cell-specific reproductive measure before and four times after the intervention (6, 12, 18 and 24 months). Compared to the e-Book group the CHOICES group had significantly more improvement in knowledge over time (p = .004) but not intention (p = .18) or behavior (p = .69). At baseline, 114 (48.7 %) participants reported having partners who would not put the couple at risk for their children inheriting SCD. Of the 116 (49.6 %) at-risk participants, a higher poroportion of those who were in the CHOICES group chose partners that reduced their risk by the last visit than the e-Book group (p = .04). Study findings provide important insights for designing a national trial of the CHOICES intervention focusing on subjects whose partner status puts them at risk for having a child with SCD.