Musculoskeletal pain (MSP) is one of the most prevalent conditions among global medical students, affecting their daily lifestyle. In this study, we seek to determine the prevalence of MSP and its associated risk factors in a sample of medical students at Misr University for Science and Technology, Egypt. A cross-sectional study was conducted between December 2023 and February 2024, with asample size of 1472 students who filled out a modified version of the Standardized Nordic Questionnaire. Demographic variables, study hours, and special habits were collected and analyzed. The prevalence of MSP in the past week and year was documented and analyzed using common risk factors. A total of 971 responses were considered for analysis (66% of the total sample size and 27.7% of the total medical students). The majority were between 18 and 25 years old, with 50.7% males and 49.3% females. The median age was 21 (20-23) years. Most of the students were in their fifth year (23.8%). The prevalence of at least one MSPsite was 459 (47.2%) in the past week and 702 (72.2%) in the past year. MSP in the past year was significantly associated with females (OR = 2.45, 95% CI = 1.82-3.3, p = 0.001) and those with a family history of autoimmune disease (OR = 2.19, 95% CI = 1.3-3.5, p = 0.001), while it was significantly associatedin the past week with females(OR = 1.72, 95% CI = 1.3-2.2, p = 0.001) and those with a personal history of autoimmune disease (OR = 2.26, 95% CI = 1.09-4.7, p = 0.025). In the past year, neck pain was significantly associated with females (OR = 1.83, 95% CI = 1.42-3.27, p = 0.001) and those with a family history of autoimmune disease (OR = 1.4, 95% CI = 1.01-2.08, p = 0.047). Students living inside October city were less likely to have neck pain in the past yearthan those who lived outside October city(OR = 0.73, 95% CI = 0.56-0.94, p = 0.017). Shoulder pain in the past year was significantly associated with females (OR = 2.9, 95% CI = 2.1-3.98, p = 0.001) and those with a family history of autoimmune disease (OR = 1.9, 95% CI = 1.28-2.81, p = 0.001) while back pain in the past year was significantly associated with females (OR = 2.1, 95% CI = 1.6-2.7, p = 0.001). Gender was the only factor that was associated with MSP on multivariate regression analysis for the past week (p = 0.001) and past year (p = 0.001). MSP is highly prevalent among medical students in Egypt, especially females, those with a personal history of autoimmune disease, and those with a family history of autoimmune disease. Despite the high prevalence and the effect on daily lifestyle, very few medical students sought help. More studies are needed to evaluate other risk factors and effective approaches to alleviate MSP among medical students in Egypt.