Introduction: In the complex setting of a medical school it becomes essential to utilize an approach to teaching and learning that is best suited to the needs of the students. In developing countries like India, where there is an exponential increase of institutions catering to medical students, it becomes a challenge to teach to large number of students per class. Hence, research is needed to identify the needs of students in relation to their day to day learning activities. Objectives: To understand the preferences and perception of medical students about the current methods of teaching, aids used for teaching and also identify barriers in learning as perceived by the students. Method: A Cross-sectional study was carried out at Kasturba Medical College, Mangalore during May 2012. Study participants included 2 nd and 3 rd year medical students. A semi-structured questionnaire was used to collect the information in relation to preferences and perceptions regarding teaching methods utilized for theory and clinical teaching. SPSS version 11.5 was used for analysis of data. The association between variables of interest was tested using Chi-square test. Results: A total of 286 students (56.6 % females and 43.4% males) participated with a dropout rate of 10.6%. The study revealed that 71.3% of the students had an attendance above 75%. The most preferred teaching method was Problem Based Learning (PBL) (71.4%) as students felt that it enhanced lateral thinking while Didactic Lectures was the least preferred (32.8%). The most preferred modality of teaching aid was found to be Black board preferred by 46.9% students. In learning rare signs and cases, students preferred video lectures (41%) and mannequins (75.9%) in learning clinical skills. The main barrier in theory learning identified was inappropriate teaching methods (15%) and being new to clinical posting (38.5%) in case of learning clinical skills. Conclusion: The findings of the study suggest that a combination of traditional methods with other methods such as PBL, video lectures and mannequins could be an effective way of teaching theory and clinical skills.