Objective: To study and compare the prevalence of musculoskeletal pain in Medical and non-medical students and find out the specific factors associated with the occurrence of this pain. Methodology: This is a cross-sectional study from March-May 2017 where a total of 400 medical and 350 non-medical students were registered using a structured questionnaire made by modification of Nordic questionnaire. Characteristics of musculoskeletal pain were determined Pain was also graded by using a grading scale. Results: Mean age for medical and non-medical students was 21.36 and 20.97 respectively. The prevalence of musculoskeletal pain was higher among females. More data were collected from 2nd and 5th year of medical and 1st and 2nd year of non-medical students. High incidence was found in medical students with occurrence mostly in Neck. This frequency of musculoskeletal pain was quiet high during the last 7 days. The long study hours and use of computer/laptop were found to be greater among medical undergraduates but no significant association was found in medical unlike non-medical students. Majority of undergraduate students reported a normal BMI. Our study has found no co-relation of BMI with prevalence of pain. It was also observed that medical students with musculoskeletal pain spent more time on travelling when compared to non-medical. Association was found with the use of back packs. The study observed the level of many daily activities like exercise and outdoor sports etc. but no significant relation was found. Conclusion: Prevalence of musculoskeletal pain among undergraduate students is truly high, more so in medical students. Medical students have shown no association of studying for long hours and use of computer/laptop with musculoskeletal pain when compared to non-medical students. More studies should be done to know contributing factors of musculoskeletal pain among undergraduate students.