The healthcare industry is one of the main industries with a high prevalence of musculoskeletal disorders (MSDs). Surgical practice mostly involves repetitive tasks with fine motor control, precise motions, high levels of mental concentration, and close visual focus. This cross-sectional study aimed to define the prevalence and risk factors of MSDs and visual problems among physicians. One hundred surgical physicians and one hundred medical physicians were involved in the study. Both groups underwent assessment of socio-demographic and occupational history, alongside evaluation for musculoskeletal and visual problems. The study revealed a significantly higher prevalence of MSDs, particularly neck and back pain, as well as blurred near vision and eye dryness, among surgical physicians compared to medical physicians. Risk factors for these conditions included long working hours (≥30 h/week) in clinics or operating rooms, as well as using endoscopes and microscopes/loupes during surgery. In conclusion, MSDs and visual problems were prevalent among physicians, particularly surgical physicians. Integrating ergonomic principles across all domains of healthcare and promoting healthcare worker awareness through training and intervention programs are crucial steps in addressing these issues.