Background: Childhood obesity is a significant but largely "modifiable" health risk, disproportionately affecting socioeconomically disadvantaged, racial/ethnic minority, and rural children. Elementary school-aged children typically experience the greatest increases in excess weight gain and therefore are important targets for reducing adolescent and adult obesity while improving children's health. Our study evaluated outcomes of a 3-year elementary school-based program for reducing obesity in American Indian and White students attending eight rural schools in the U.S. upper Midwest. Method: Researchers measured body mass indexes (BMI) and other health indicators and behaviors of 308 beginning third-grade students and then again at the end of students' third, fourth, and fifth grades. The primary focus of this study is a mixed multilevel longitudinal model testing changes in age- and gender-adjusted BMI z scores (zBMI). Results: There was a significant decrease in zBMI across the 3-year study period. Ethnicity analyses showed that White students had overall decreases in zBMI whereas American Indian students' zBMIs remained stable across the program. Comparisons with children from an age- and cohort-matched national sample provided support for the effectiveness of the school program in reducing BMI and obesity during the study period. Conclusion: An elementary school-based health program that addresses a range of students' obesity-related health behaviors, the school health environment, and that involves educators and parents is an effective intervention for reducing or stabilizing BMI in rural White and American Indian students. School health programs for students living in rural communities may be especially effective due to greater school and community cohesiveness, and valuing of the school's primary role in improving community health.