Background: The School Health Policies and Programs Study (SHPPS) 2006 examined 8 components of school health programs: health education, physical education and activity, health services, mental health and social services, nutrition services, healthy and safe school environment, faculty and staff health promotion, and family and community involvement. All 8 components were assessed at the state, district, and school levels. Two components, health education and physical education and activity, also were assessed at the classroom level. Methods: Computer-assisted telephone interviews or self-administered mail questionnaires were completed by state education agency personnel in all 50 states plus the District of Columbia and among a nationally representative sample of school districts (n = 538). Computer-assisted personal interviews were conducted with personnel in a nationally representative sample of elementary, middle, and high schools (n = 1103), with a nationally representative sample of teachers of required health education classes or courses (n = 912), and with a nationally representative sample of teachers of required physical education classes or courses (n = 1194). Results: This article provides a detailed description of the development of the questionnaires; sampling; data collection; and data cleaning, weighting, and analysis. Conclusions: SHPPS 2006 is the largest and most comprehensive study of school health programs ever conducted. Fielding a study of this magnitude provides many challenges, and several recommendations for future studies emerged from the experience. (Contains 6 tables.)