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This article explores the spatio-temporal structure of infectious diseases in modern Japan, using measles mortality data from the late nineteenth and early twentieth centuries. Three aspects of the epidemiology of measles are discussed: the synchronization of epidemic waves, seasonality, and age at infection. These epidemiological analyses are connected to, respectively, regional integration, governmental policy on primary school education, and the number of young children in families. In addition, based on the fact that measles did not become endemic in early modern Edo (Tokyo), this article corrects epidemiologists’ misunderstanding about the threshold of endemicity and argues that the critical population size varied substantially according to the societal factors of a given community. In so doing, this article suggests that historians can use measles data as a new biometric index for studying human health and socio-economic conditions in societies of the past.