OBJECTIVE: To determine the prevalence and associated factors for personal, work-related and patient/client-related burnout in clinical professionals and biomedical scientists in academic medicine. DESIGN: Prevalence survey using the Copenhagen Burnout Inventory. SETTING: Mid-size academic health centre. PARTICIPANTS: Clinical providers (n=6489) and biomedical scientists (n=248) were invited to complete the survey. 1646 completed responses (response rate 24.4%) were analysed. PRIMARY AND SECONDARY OUTCOME MEASURES: Prevalence estimates and adjusted ORs (AOR) were stratified for gender, age and professional category. RESULTS: Type of burnout varies across professional categories, with significant differences between clinicians and scientists. The prevalence of personal burnout was 52.7% (95%CI 50% to 55%), work-related burnout 47.5% (95%CI 45% to 49%) and patient/client-related burnout 20.3% (95%CI 18% to 22%). The prevalence of personal and work-related burnout was higher among women, while those aged 20-30 had a higher prevalence of all three burnout categories. Overall, clinical professionals had higher personal and work-related burnout, while biomedical scientists had higher client-related burnout. Accounting for the effects of gender and age, a significantly higher risk for personal burnout was found for physicians (AOR 1.64; 95%CI 1.3 to 2.1) and nurses (AOR 1.5; 95%CI 1.03 to 2.2). Significantly higher odds of work-related burnout were found for nurses (AOR 1.5; 95%CI 1.2 to 1.9) and residents (AOR 1.9; 95%CI 1.04 to 3.6). Basic scientists (AOR 10.0; 95%CI 5.7 to 17.6), physicians (AOR 2.8; 95%CI 1.9 to 4.1) and nurses (AOR 2.1; 95%CI 1.3 to 3.5) had higher odds of patient/client-related burnout. CONCLUSIONS: Types of burnout are unevenly distributed in academic medical centres. Physicians have higher risk of personal and patient/client-related burnout, residents have higher risk of work-related burnout, basic scientists are at higher risk of client-related burnout and nurses have higher odds of all three types of burnout. Interventions addressing the problem of burnout in clinical environments may be inadequate to support biomedical scientists.