The purpose of this paper is to describe the rationale, design, methods and baseline results of the Family Spirit trial. The goal of the trial is to evaluate the impact of the paraprofessional-delivered "Family Spirit" home-visiting intervention to reduce health and behavioral risks for American Indian teen mothers and their children. A community based participatory research (CBPR) process shaped the design of the current randomized controlled trial of the Family Spirit intervention. Between 2006 and 2008, 322 pregnant teens were randomized to receive the Family Spirit intervention plus Optimized Standard Care, or Optimized Standard Care alone. The Family Spirit intervention is a 43-session home-visiting curriculum administered by American Indian paraprofessionals to teen mothers from 28 weeks gestation until the baby's third birthday. A mixed methods assessment administered at nine intervals measures intervention impact on parental competence, mother's and children's social, emotional and behavioral risks for drug use, and maladaptive functioning. Participants are young (mean age = 18.1 years), predominantly primiparous, unmarried, and challenged by poverty, residential instability and low educational attainment. Lifetime and pregnancy drug use were ~2-4 times higher and ~5-6 times higher, respectively, than US All Races. Baseline characteristics were evenly distributed between groups, except for higher lifetime cigarette use and depressive symptoms among intervention mothers. If study aims are achieved, the public health field will have new evidence supporting multi-generational prevention of behavioral health disparities affecting young American Indian families and the utility of indigenous paraprofessional interventionists in under-resourced communities.