Background: The public health reform in Chile resulted in changes in working conditions and organization of health centers. Aim: To examine the presence of psychophysiological symptoms in professionals of public hospitals in the Metropolitan Region and their association with current working conditions. Material and Methods: A questionnaire of quality of working life was applied to a sample of 80 physicians and 110 nurses. The questionnaire considers scales and open questions. Results: Nurses had a higher level of discomfort than physicians (p < 0.01) and had significantly higher scores for emotional distress, physical fatigue, digestive disorders, headache, insomnia, back pain and muscle tension (p < 0.01). There were statistically significant negative correlations between psychophysiological distress and working conditions (r = -0.418), social climate (r = -0.395), satisfaction with the organization (r = -0.337) and psychosocial well-being (r = -0.267). A regression model showed that 21% of the variance in psychophysiological distress was explained by working conditions, psychosocial well-being and adaptation to the organization. Conclusions: There is a relationship between the high prevalence of psychophysiological symptoms and bad working conditions of public health professionals.