<strong>Objective</strong> The objective of this study was to evaluate the perception, attitudes, and barriers faced by students during the online anatomy course. <strong>Materials and methods</strong> A descriptive cross-sectional study was carried using a questionnaire, based on available feedback questionnaires from the faculty and published questionnaires, pilot tested and finalized. It was distributed via Google-forms to 185 second-year students who had undergone 2 semesters of online teaching. <strong> </strong> <strong>Results</strong> A total of 115 Google-forms were received. Females represented 50.9%, with a mean age of 21.9±1.022 years. Smartphones (86%) were mainly used to access online material while mobile data (79.8%) was the commonest method of internet access. Online learning tool usage was: Moodle-98.2% Zoom-94.7% and Youtube-66.7%. Attitudes towards online learning were positive (77.2%) with prior preparation for teaching sessions as high as 97.4% and active participation in the online sessions (81.6%). Majority preferred Moodle for online lectures (81.74%), histology practical sessions (89.57%) and slide projections (82.74%) while for gross practical sessions it was Moodle (80.87%) and Youtube (41.74%). For tutorials (70.44%) and discussions (76.52%) majority preferred Zoom sessions. Of the respondents 57.9% feared lack of direct anatomy learning might have an impact on their clinical skills in future. The major problems of online learning were identified as lack of self-motivation, lack of onsite practicals, and increased screen time. <strong>Conclusion</strong> Though majority of participants agreed that onsite anatomy teaching and learning cannot be replaced by the online course, the attitude towards it appears to be mostly positive during the COVID-19 pandemic.