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Description: Despite the fact that there are several researchers reporting the risks of doctoral students in terms of mental health, there is still a lack of studies exploring their well-being at an organizational level, looking at the difference between male and female PhD students. This work aims at describing gender differences in the organizational well-being of doctoral students in an Italian context. A sample of 121 Italian PhD students filled an adaption of the ANAC questionnaire (National Au-thority for Anti-Corruption) for an organizational well-being assessment between June and July 2021. The results show that there are a number of well-being indicators for which female PhD students have statistically lower scores than men regarding: (1) the perception of health and safety at work; (2) career development; and (3) job autonomy. Practical suggestions to improve the academic system in terms of sustainability for preventing PhD students’ organizational malaise with a particular focus on gender equality are provided.