Accurate evaluation and documentation of the efficacy of recovery schools can be vital to the continuation and expansion of these beneficial resources. A very limited data set currently exists that examines the value of specific schools established to support adolescents and young adults in recovery; additional research is necessary. The following article outlines the methodology utilized in a current quasi-experimental study evaluating both academic and therapeutic outcomes of adolescents attending recovery high schools as compared to traditional (non-recovery-based) high schools. The developmental considerations in assessing adolescents in recovery and their parents is delineated in this article, which underscores the need for extensive knowledge of adolescent substance abuse and other mental health issues. In addition, sensitivity around privacy among adolescents, parents, schools, and health providers is highlighted, as well as the validity of assessment. Key assessment strategies, including protocol of recruitment and interviewing techniques, are also presented along with a list of parent and adolescent assessment instruments and their corresponding interpretive variables. Protocol recommendations for future research are also outlined.