Problem Based Learning has been implemented worldwide, with no exception including Indonesia. Faculty of Medicine, Universitas Indonesia (FMUI) has implemented PBL as one of learning approaches since 2005. Therefore, we would like to evaluate the effectiveness of this program by exploring students' perceptions on PBL implementation. A single case study with multiple unit of case analysis was conducted. Two to six students representing the 2nd, 4th, 6th, 8th and 10th semester of FMUI students were recruited voluntary to participate in this study. A structured focus group discussion (FGD) was moderated by one to two staff members. Data collected were then transcribed, coded, categorized and analysed qualitatively to construct a concept. Students' understanding of PBL was still varied. A concept of PBL implementation at our institution was developed based on students' perceptions. We can not adopt PBL implementation in the same way as the Western countries institutions did. To implement PBL successfully, we should prepare and consider many aspects including cultural background.