Despite the rapid expansion of interest in competency-based assessment, few descriptions of assessment systems specifically designed for a competency-based curriculum have been reported. The purpose of this article is to describe the design of a portfolio approach to a comprehensive, competency-based assessment system that is fully integrated with the curriculum to foster an educational environment focused on learning. The educational design goal of the Cleveland Clinic Lerner College of Medicine of Case Western Reserve University was to create an integrated educational program-curriculum and instructional methods, student assessment processes, and learning environment-to prepare medical students for success in careers as physician investigators. The first class in the five-year program matriculated in 2004. To graduate, a student must demonstrate mastery of nine competencies: research, medical knowledge, communication, professionalism, clinical skills, clinical reasoning, health care systems, personal development, and reflective practice. The portfolio provides a tool for collecting and managing multiple types of assessment evidence from multiple contexts and sources within the curriculum to document competence and promote reflective practice skills. This article describes how the portfolio was developed to provide both formative and summative assessment of student achievement in relation to the program's nine competencies.