In spite of significant disparities in sexual health outcomes for American Indian youth, no studies exist examining the effectiveness of HIV-prevention interventions. Circle of Life is an HIV-prevention intervention specifically developed for American Indian middle-school youth. We describe the rationale, methodology, and baseline results of a longitudinal randomized trial of Circle of Life conducted among American Indian youth aged 11–15 in a reservation community. The innovative design includes two pre-intervention waves to determine patterns of behavior prior to the intervention that might be associated with a differential impact of the intervention on sexual risk. We used one-way analysis of variance and chi-square tests to test for significant differences between randomized group assignment at each baseline wave and generalized estimating equations (GEE) to test significant differences in the rate of change in outcomes by group longitudinally. We present the collaborative and adaptive strategies for consenting, assenting, and data collection methodology in this community. Achieved response rates are comparable to other similar studies. Results from the two baseline waves indicate that few outcomes significantly varied by randomized intervention assignment. Ten percent of youth reported having had sex at Wave 1, rising to 15% at Wave 2. Among those who had had sex, the majority (>70%) reported using a condom at last sex. The project is well positioned to carry out the longitudinal assessments of the intervention to determine the overall impact of the Circle of Life and the differential impact by pre-intervention patterns of behavior across youth.