Background: COVID-19 pandemic has created the largest disruption in education systems in history. Numerous medical institutions have shifted to online teaching with the hope to reduce viral transmission. Objectives: To compare the effectiveness of online teaching and traditional teaching in the domains of collaborative learning, critical thinking skills and social interaction and to describe the advantages and difficulties faced in online learning by MBBS students. Materials and Methods: An online-based cross-sectional study was conducted from May 2021 to August 2021 in a private medical college in Salem district of Tamil Nadu, India. Among the 600 MBBS students attending online classes from the first year to final year MBBS, 574 students consented to the study through mail and were studied using a semi-structured questionnaire prepared in Google form and sent through mail. Descriptive analysis was done and the association between the categorical variables were tested using chi-square test. Results: Traditional way of teaching was perceived to improve the critical thinking skills (p <0.0006), social interaction skills (p<0.044) and collaborative learning (p <0.01) more than online teaching. Advantages of online teaching identified were comfortable learning environment (38%) easier for slow learners (19%), learning at their own pace (18%) etc. Difficulties faced in online teaching were technical difficulties (62%), lack of self-motivation (61%), time management (56%) etc. Conclusion: Challenges faced by the students need to be identified earlier and Governments/educational institutions can focus more on removing the barriers to connectivity. © 2022 Elsevier B.V., All rights reserved.