The aim of this study was to estimate the prevalence of anxiety and depression symptoms in health professionals in high-complexity services and the associated factors. Epidemiological, cross-sectional, analytical study. The Beck Anxiety and Depression Inventories and a questionnaire with sociodemographic and occupational aspects, health conditions, lifestyle and quality of life were used. A total of 490 professionals participated. The prevalence of anxiety and depression symptoms was 26.5% and 19.8%, respectively. The prevalence of anxious symptoms was lower among nurses and physicians, was higher among female professionals, who used sleep medications, with altered fasting blood glucose levels, with a good and regular/need to improve lifestyle, and with scores below average in the social relationships domain. The prevalence of depression symptoms was higher in females, who took time off work due to stress, depression, or anxiety, had a good and regular/need to improve lifestyle, and had below-average scores in the psychological and environmental domains. The outcomes investigated were associated with the following variables: gender, professional category, use of sleep medication, fasting glucose, stress leave, depression or anxiety, lifestyle, and quality of life.