Abstract Background The percentage of temporary workers in the workforce has increased in many European countries. The working environments of temporary workers are often characterized by job insecurity and exposure to hazardous working conditions. Studies have investigated the health status of this population but few of them have specifically investigated work-related diseases. The aim of this study is to compare the risk of uncompensated work-related diseases (UWRD) in temporary workers with permanent contract workers in France between 2009 and 2014. Methods UWRD and suspected associated exposure factors were notified by occupational physicians involved in French UWRD surveillance programme. Sociodemographic and professional characteristics were recorded for all salaried workers consulted by occupational physicians. We analysed musculoskeletal (MSD) disorders (elbow, hand/wrist, shoulder, back) and mental health disorders (MHD) according the type of consultation (periodic check-up, hiring...) using logistic regression. The distributions of notified exposure factors for MSD and MHD were compared between temporary and permanent workers. Results Of the 433 148 salaried workers consulted as part of the surveillance programme, 5.3% and 80.2% had temporary and permanent contracts, respectively. Temporary workers were as likely to have work-related shoulder, elbow and hand/wrist MSD as permanent workers. The former had a lower risk of MHD irrespective of the type of consultation (OR = 0.4, 95 % CI 0.3-0.5) and a lower risk of back MSD during on-demand/return-to-work consultations (OR = 0.2, 95% CI 0.1-0.5) and during periodic check-ups (OR = 0.3, 95% CI 0.2-0.7). Conclusions Temporary workers were not at a higher risk of UWRD (MSD and MHD) than permanent workers. This suggests that the generally poor health status found in temporary workers in previous studies may be linked more to their general health status and perceived job insecurity than to poorer working conditions. Key messages In our study, the risk of work related musculoskeletal disorders and mental health disorders in temporary workers was no greater than that in permanent workers. Poor general health known in temporary workers, may be linked more to their general health status, job insecurity and decreasing career trajectory than to poorer working conditions.