BACKGROUND: Musculoskeletal disorders (MSDs) are prevalent in working populations and could result in a number of detrimental consequences. In China, healthcare professionals (HCP) in large hospitals may be likely to suffer from MSDs considering the facts of shortages in medical staff, the large Chinese population base, the aging of the population and patients' inclination to go to large hospitals. This study aimed to determine the prevalence and factors associated with MSDs among HCP working in tertiary hospitals. METHODS: A self-administered questionnaire incorporating the Nordic Musculoskeletal Questionnaire and the Dutch Musculoskeletal Questionnaire was conducted among 14,720 HCP in eight tertiary hospitals selected by random cluster sampling in Shandong, China. Multivariable logistic regression analysis was used to quantify the association of psychological, ergonomic, organizational and individual factors with MSDs. RESULTS: The 12-month period prevalence rate of experiencing an MSD in at least one body region for at least 24 h, experiencing an MSD for at least three months, and seeking health care for this condition were 91.2, 17.1 and 68.3%, respectively; these rates were highest for the lower back (72.8, 14.3, 60.3%) and knees (65.7, 8.1, 46.7%), followed by the shoulders (52.1, 6.2, 38.9%), neck (47.6, 4.8, 32.6%), wrists/hands (31.1, 3.2, 23.1%), ankles/feet (23.6, 1.9, 13.4%), upper back, hips/thighs and elbows. MSDs were associated with workload (work hours per week, break times during workday), psychological factors (psychological fatigue, mental stress), employment status and ergonomic factors. Regarding the ergonomic factors, lower back MSDs were associated with bending the trunk frequently, heavy or awkward lifting, and bending or twisting the neck; knee MSDs were associated with walking or standing for long periods of time; and shoulder MSDs were associated with maintaining shoulder abduction for long periods of time and bending or twisting the neck. CONCLUSIONS: MSDs among HCP in tertiary hospitals in Mainland China were highly prevalent. The many factors listed above should be considered in the prevention of MSDs in HCP.