PURPOSE: Portfolios are a powerful tool to collect and evaluate evidence of medical students' competence across time. However, comprehensive portfolio assessment systems that are implemented alongside traditional graded curricula at medical schools in the United States have not been described in the literature. This study describes the development and implementation of a longitudinal competency-based electronic portfolio system alongside a graded curriculum at a relatively large U.S. medical school. METHOD: In 2009, the authors developed a portfolio system that served as a repository for all student assessments organized by competency domain. Five competencies were selected for a preclerkship summative portfolio review. Students submitted reflections on their performance. In 2014, four clinical faculty members participated in standard-setting activities and used expert judgment and holistic review to rate students' competency achievement as "progressing toward competence," "progressing toward competence with some concern," or "progressing toward competence pending remediation." Follow-up surveys measured students' and faculty members' perceptions of the process. RESULTS: Faculty evaluated 156 portfolios and showed high levels of agreement in their ratings. The majority of students achieved the "progressing toward competence" benchmark in all competency areas. However, 31 students received at least one concerning rating, which was not reflected in their course grades. Students' perceptions of the system's ability to foster self-assessment were mixed. CONCLUSIONS: The portfolio review process allowed faculty to identify students with a concerning rating in a behavioral competency who would not have been identified in a traditional grading system. Identification of these students allows for intervention and early remediation.