The purpose of this study was to estimate the prevalence of suspected cases of common mental disorders (CMD) on Brazilian civil aviation pilots and to investigate associations between CMD, demographics, and labor variables.A quantitative cross-sectional study was conducted on 807 working pilots between October 2009 and October 2010 using a self-administered questionnaire to obtain sociodemographic data and information about workload. CMD prevalence was estimated with the Self-Reporting Questionnaire-20 items (SRQ-20). Multiple logistic regression was used in statistical data analyses.The overall prevalence of CMD was 6.7% with the cutoff point of 8 used in this study, i.e., scores greater than or equal to 8 in SRQ-20 define positive cases. Using alternative cutoffs, the prevalence was 9.2% (cut off point 7) or 12% (cutoff point 6). Among the individuals who did not exercise, 10.2% presented suspected CMD. Among those with a heavy workload, 23.7% presented scores indicating suspected CMD. Only variables relating to workload and the practice of physical activity were significantly correlated with the estimate of CMD after multivariate analysis. Regular physical exercise afforded a possible protective effect against suspected cases of CMD, while there was a higher prevalence of suspected cases among subjects with heavy workloads.The inclusion of the topic of mental health among the targets and priorities of civil aviation in Brazil is imperative. Addressing issues such as the regular practice of physical activity and workload can contribute to achieving a better balance between flight safety and productivity.