The authors describe the development of a theory-driven assessment and research protocol at the Adolescent Treatment Program of The Menninger Clinic. First, the theoretical framework behind a mentalization-based model for assessment and treatment is described. Next, the process whereby measures were selected to operationalize key components of the mentalization-based model is discussed, including a brief discussion of each measure and assessment procedure. The next section describes the clinical and research use of the data collected. Here, the authors describe how outcomes assessment information is integrated into the clinical decision-making process, and they outline the research questions they aim to answer through the assessment protocol. The authors conclude with a section on the challenges, pitfalls, and future directions of the project.