The present study randomly assigned 15 Bahamian elementary schools to one of three intervention conditions. To assess the adequacy of cluster randomization, we examined two concerns identified by the local research team: inequality of gender distribution and environmental risk among groups. Baseline significant differences in risk and protective behaviors were minimal. There were significantly more males in the intervention group. Males had higher rates of risk behavior at all assessments. Poor school performance was also higher among the intervention condition and was significantly associated with increased rates of many but not all risk behaviors. Prior to adjusting for gender and school performance, several risk behaviors appeared to be higher after intervention among intervention youth. Adjusting for gender and school performance eradicated the group differences in risk behavior rates. Results demonstrate the importance of adequate randomization where outcomes of interest are rare events at baseline or differ by gender and there is an unequal gender distribution and the importance of the local research team's knowledge of potential inequalities in environmental risk (i.e., school performance). Not considering such individual differences could impact the integrity of trial outcomes.