Background. Microsurgery is a surgical procedure requiring a high degree of precision and is commonly facilitated through the use of an intraoperative microscope. When operating the microscope system, the long-term posture leads to musculoskeletal disorders in surgeons, and seats are commonly employed to diminish these problems. The present study was conducted to evaluate musculoskeletal discomfort during work with a saddle seat in comparison with conventional seats for microscopic work. Methods. Two types of seats, a saddle and a conventional one, were evaluated for 73 microsurgical surgeons in terms of musculoskeletal discomfort. Corlett and Bishop's body part discomfort scale was used to assess musculoskeletal discomfort before and after working with the seats. Results. The highest amount of discomfort that microsurgical surgeons acquire in the workplace was focused on their neck, shoulders, arms and back. During work with a saddle seat, a significant reduction was found for discomfort values in the neck, shoulder, arm, back, elbow and forearm, as well as the whole body (p < 0.05). Conclusion. This study showed that the use of saddle seats provides a more appropriate physical posture at work, and can decrease musculoskeletal discomfort in different parts of the body of microsurgical surgeons.