Introduction: Work-related musculoskeletal disorders (MSDs) are caused by a variety of environmental and organizational workplace factors, which makes them some of the most commonly reported work-related health problems in Europe and the world. Our purpose was to determine the prevalence of musculoskeletal complaints among employees in higher education, as well as the most significant risk factors for their occurrence. Material/Methods: The survey was conducted among 542 employees of Trakia University, Bulgaria, using questionnaires on symptoms and exposure to the most common occupational risk factors for MSDs. The subjects were grouped and compared by gender, age, years of service and employment position. Results: 74% of participants reported one or more musculoskeletal complaints, with the most common locations being the lower and upper back, neck, and shoulders. Women had a significantly higher average number of complaints (2.41) than men (1.64), p = 0.000058. A higher percentage of hand/arm MSDs was reported by auxiliary workers, and lower back complaints were more frequently reported by administrative staff, compared to other groups. A positive correlation was found between the number of MSDs and the years of service (r=0.11, p=0.019), but not between MSDs and age. The major reported workplace risk factors for MSDs were working with display screen equipment (55.9% of respondents), frequent, repetitive hand movements (37.46%), and non-ergonomic workstations/arrangements (27.67%). Conclusions: Prevention of MSDs of occupational origin requires a comprehensive approach involving the identification, assessment and control of a number of ergonomic and organizational factors. Similar studies in other occupational groups would help to better understand and prevent these chronic, painful and often disabling diseases.