BACKGROUND Many students attending ENT clinical postings were found to have difficulty in conceptualising the 3-dimensional (3 D) anatomy of the ear, nose and throat. Students in project-based learning (PBL) classrooms obtained higher scores than students in traditional classrooms. PBL using clay model and modelling compound have been successfully used to improve the 3 D anatomical understanding in medical students. The purpose of this study was to compare the effectiveness of PBL over lecture in the acquisition of 3 D anatomical knowledge among third-year undergraduate medical students and also to understand the student perception towards PBL. METHODS This quasi-experimental study was done at GMC, Ernakulam among 84 third-year undergraduate medical (MBBS) students who had given consent for the study. They were divided into 3 batches according to roll numbers (28 students in each). Two topics in ENT anatomy were selected. 14 students of one batch attended lecture class, while the remaining 14 attended PBL class. This was repeated for the remaining two batches. In the next week, a cross-over was given for the second topic. Pre-test and post-test for both topics were administered to all the students before and after the sessions. Feedback regarding the student perceptions about PBL was obtained. RESULTS There was a statistically significant difference between the mean of pre-test and post-test scores (p values of 0.001) in both lecture and PBL groups in both topics. The mean of pre-test scores of the lecture group and PBL in both topics did not show any significant difference. There was a statistically significant difference between the mean of post-test scores in the case of nose topic (p value 0.004). 88% of students had a favourable view of PBL as a teaching methodology. There was no statistically significant difference across the genders in their perception of the PBL as a teaching-learning method. (p value 0.314) CONCLUSIONS The study shows that both PBL and lecture brought about significant change in the knowledge level of the student. The students had a favourable opinion regarding PBL as a teaching method. However, PBL was not found to be more beneficial than conventional lecture in the acquisition of knowledge. KEY WORDS Anatomy Education; Medical Education; Project-Based Learning; Didactic Lecture.