Background: Clinical reasoning is an essential skill to be learned during medical education. A developmental framework for the assessment and measurement of this skill has not yet been described in the literature. Objective: The authors describe the creation and pilot implementation of a rubric designed to assess the development of clinical reasoning skills in pre-clinical medical education. Design: The multidisciplinary course team used Backwards Design to develop course goals, objectives, and assessment for a new Clinical Reasoning Course. The team focused on behaviors that students were expected to demonstrate, identifying each as a 'desired result' element and aligning these with three levels of performance: emerging, acquiring, and mastering. Results: The first draft of the rubric was reviewed and piloted by faculty using sample student entries; this provided feedback on ease of use and appropriateness. After the first semester, the course team evaluated whether the rubric distinguished between different levels of student performance in each competency. A systematic approach based on descriptive analysis of mid-and end of semester assessments of student performance revealed that from mid-to end-of-semester, over half the students received higher competency scores at semester end. Conclusion: The assessment rubric allowed students in the early stages of clinical reasoning development to understand their trajectory and provided faculty a framework from which to give meaningful feedback. The multidisciplinary background of the course team supported a systematic and robust course and assessment design process. The authors strongly encourage other colleges to support the use of collaborative and multidisciplinary course teams.