Implementation of a pedagogical approach is a continuous and evolving process. As an institution with more than 15 years problem-based learning (PBL), we studied how the learning and teaching processes are currently practiced in a 2-year preclinical basic sciences program to assess whether they still match the intended objectives. Using both students' and tutors' evaluations, we analyzed and compared their perceptions on the program content and its organization, on tutors' functioning and on the duration of PBL sessions throughout 11 instructional units of the second and third-year of a 6 years medical curriculum. Whereas both tutors and students indicated that the content and problems selected for the curriculum were well adapted to the PBL process, they felt the references as well as the self-study time as moderately appropriate. Over the course of the 2-year program, tutorial sessions got linearly shorter, whereas reporting sessions got longer. While tutors knew well the PBL approach and were suitably prepared to their tutorials, they however, became less regular in providing feedback and in evaluating group functioning over the 2 years. Our results suggest that the practice of the PBL process evolves within and throughout a 2-year preclinical program and moves away from the original intentions. Possible underlying reasons and their implications are discussed within the context of tutors' and students' concepts of teaching and learning, the medical schools' learning environment and teaching practices and the difficulty of developing and maintaining in the long term a deep and self-directed learning approach.