<jats:p>In complex systems such as hospitals, work organization can influence the level of occupational stress and, consequently, the physical and mental health of workers. Hospital healthcare workers were asked to complete a questionnaire during their regular occupational health examination, in order to assess the perceived level of organizational justice, and to verify whether it was associated with occupational stress, mental health, and absenteeism. The questionnaire included the Colquitt Organizational Justice (OJ) Scale, the Karasek/Theorell demand-control-support (DCS) questionnaire for occupational stress, and the General Health Questionnaire (GHQ12) for mental health. Workers were also required to indicate whether they had been absent because of back pain in the past year. Organizational justice was a significant predictor of occupational stress. Stress was a mediator in the relationship between justice and mental health. Occupational stress was more closely related to perceptions of lack of distributive justice than to perceptions of procedural, informational, and interpersonal justice. Physicians perceived significantly less distributive justice than other workers. In adjusted univariate logistic regression models, the perceptions of organizational justice were associated with a significant reduction in the risk of sick leave for back pain (OR 0.96; CI95% 0.94–0.99; p < 0.001), whereas occupational stress was associated with an increased risk of sick leave (OR 6.73; CI95% 2.02–22.40; p < 0.002). Work organization is a strong predictor of occupational stress and of mental and physical health among hospital employees.</jats:p>