The Safe Schools/Healthy Students (SS/HS) national evaluation seeks to assess both the implementation process and the results of the SS/HS initiative, exploring factors that have contributed to or detracted from grantee success. Each site is required to forge partnerships with representatives from education, mental health, juvenile justice, and law enforcement, coordinating and integrating their efforts and working together to contribute to comparable outcomes (e.g., reduced violence and alcohol and drug use, improved mental health services). The evaluation uses multiple data collection techniques (archival data, surveys, site visits, interviews, and focus groups) from a variety of sources (project directors, community partners, schools, and students) over several years. Certain characteristics of the SS/HS initiative represent unique challenges for the evaluation, including the absence of common metrics for baseline, outcome data, and lack of comparison group. A unifying program theory was required to address these challenges and synthesize the large amounts of qualitative and quantitative information collected. This article stresses the role of program theory in guiding the evaluation. (Contains 1 figure.)