This paper describes the process of developing a research proposal for submission to the National Institutes of Health (NIH) in collaboration with an urban public health agency. Two university-based researchers from different social science disciplines, each with previous experience in substance abuse research, invested significant time learning about the key questions and concerns of participants in several community-based programs, including clients, administrators and professionals from the county drug court, law enforcement, and substance abuse treatment and recovery services. They then developed a proposal which integrated their own academic interests with the questions and concerns that they uncovered in their preliminary research. After the proposal was written, the researchers presented it to an audience of community partners. Following the successful funding of the study, negotiations with various partners continued throughout the data collection process. The paper concludes with some suggestions for other researchers who may wish to engage in this type of applied, collaborative, interdisciplinary research.