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Background: American Indian and Alaska Native (AI/AN) youth face multiple health challenges compared to other racial/ethnic groups, which could potentially be ameliorated by the dissemination of evidence-based adolescent health promotion programs. Previous studies have indicated that limited trained personnel, cultural barriers, and geographic isolation may hinder the reach and implementation of evidence-based health promotion programs among AI/AN youth. Although Internet access is variable in AI/AN communities across the United States, it is swiftly and steadily improving, and it may provide a viable strategy to disseminate evidence-based health promotion programs to this underserved population. Objective: We explored the potential of using the Internet to disseminate evidence-based health promotion programs on multiple health topics to AI/AN youth living in diverse communities across 3 geographically dispersed regions of the United States. Specifically, we assessed the Internet’s potential to increase the reach and implementation of evidence-based health promotion programs for AI/AN youth, and to engage AI/AN youth. Methods: This randomized controlled trial was conducted in 25 participating sites in Alaska, Arizona, and the Pacific Northwest. Predominantly AI/AN youth, aged 12-14 years, accessed 6 evidence-based health promotion programs delivered via the Internet, which focused on sexual health, hearing loss, alcohol use, tobacco use, drug use, and nutrition and physical activity. Adult site coordinators completed computer-based education inventory surveys, connectivity and bandwidth testing to assess parameters related to program reach (computer access, connectivity, and bandwidth), and implementation logs to assess barriers to implementation (program errors and delivery issues). We assessed youths’ perceptions of program engagement via ratings on ease of use, understandability, credibility, likeability, perceived impact, and motivational appeal, using previously established measures. Results: Sites had sufficient computer access and Internet connectivity to implement the 6 programs with adequate fidelity; however, variable bandwidth (ranging from 0.24 to 93.5 megabits per second; mean 25.6) and technical issues led some sites to access programs via back-up modalities (eg, uploading the programs from a Universal Serial Bus drive). The number of youth providing engagement ratings varied by program (n=40-191; 48-60% female, 85-90% self-identified AI/AN). Across programs, youth rated the programs as easy to use (68-91%), trustworthy (61-89%), likeable (59-87%), and impactful (63-91%). Most youth understood the words in the programs (60-83%), although some needed hints to complete the programs (16-49%). Overall, 37-66% of the participants would recommend the programs to a classmate, and 62-87% found the programs enjoyable when compared to other school lessons. Conclusions: Findings demonstrate the potential of the Internet to enhance the reach and implementation of evidence-based health promotion programs, and to engage AI/AN youth. Provision of back-up modalities is recommended to address possible connectivity or technical issues. The dissemination of Internet-based health promotion programs may be a promising strategy to address health disparities for this underserved population. Trial Registration: Clinicaltrials.gov NCT01303575; https://clinicaltrials.gov/ct2/show/NCT01303575 (Archived by WebCite at http://www.webcitation.org/6m7DO4g7c) [JMIR Res Protoc 2016;5(4):e225]