Medical modernisation in Iran has usually been seen as politically implemented. However, this article endeavours to show that the history of medical change in Iran was a process which encompassed social, political and medical systems. Epidemics played the central role in this change by awakening social consciousness and by bringing into question the intelligibility of the ancient theories, forcing the indigenous doctors to formulate new explanations for epidemics. This led to an epistemological change in traditional medicine, which together with change in relation between medicine, politics and society under the influence of epidemics, constituted the very core of the modernisation process