American Indian and Alaska Native (AI/AN) communities harbor understandable mistrust of research. Outside researchers have historically controlled processes, promulgating conclusions and recommended policies with virtually no input from the communities studied. Reservation-based communities can apply sovereignty rights conferred by the federal government to change this research trajectory. Many tribes now require review and approval before allowing research activities to occur, in part through the development of regulatory codes and oversight measures. Tribal oversight ensures that research is directed toward questions of importance to the community and that results are returned in ways that optimize problem solving. Unfortunately, tribal governance protections do not always extend to AI/ANs residing in urban environments. Although they represent the majority of AI/ANs, urban Indians face an ongoing struggle for visibility and access to health care. It is against this backdrop that urban Indians suffer disproportionate health problems. Improved efforts to ensure responsible research with urban Indian populations requires attention to community engagement, research oversight, and capacity building. We consider strategies to offset these limitations and develop a foundation for responsible research with urban Indians.