Various disciplines in university education have used portfolios as a learning and assessment tool for competence-based education. In medical education, portfolios can be used to accommodate effective learning of medical knowledge and skills, as well as generic competencies, such as effective communication, organization, team-work and professionalism. At the Maastricht University, we have implemented a assessment system, partly based on a portfolio, for medical and generic competencies in a 4-year physician-clinical investigator master program (MD-Msc). In this program, the medical degree is combined with a clinical investigator degree, focusing on translational medicine to bridge the gap between research and care delivery by translating questions from patient care into research, and applying research results to care. In the assessment program, the portfolio is used to integrate a wide range of module assessments, progress tests, medical skills assessment and professional behaviour to assess development and progress in 4 competency domains (medical experts, scientist, health care worker and person). Students reflect regularly on strengths and weaknesses in each of the competency domains and formulate learning objectives (formative portfolios) which are discussed with a personal counselor (mentor). Throughout the program, 4 summative portfolios are assembled, which are assessed by an independent assessment committee. A drawback of our current approach is that competency-assessment is still mixed, thus regular assessments (exams) are combined with portfolio-assessment, which still skews student priority towards the regular exams. Currently, we are in the process of re-evaluating the assessment program and examining the possibility of a program-wide assessment program that is based on the portfolio alone.