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Leptospirosis is a zoonotic disease known to have wide-ranging clinical manifestations. Despite a number of published case series, culture-confirmed series are few and there is a paucity of data on Jarisch–Herxheimer reaction (JHR) associated with treatment of leptospirosis. Our objective was to describe the clinical and epidemiological factors associated with leptospirosis in an endemic area of Japan, with a focus on the occurrence of JHR, an often unrecognized and likely underestimated phenomenon.We performed a retrospective observational study of laboratory-confirmed leptospirosis at a single center over a 40-year period.We report 100 leptospirosis cases in 99 patients during the period 1974–2015. Seventy-four cases were diagnosed by culture, representing eight different serovars. JHR was seen in 23 (82%) of 28 cases, including 19 (90%) of 21 cases treated with bactericidal antibiotics compared to 4 (57%) of seven cases with bacteriostatic antibiotics (p=0.08).We found a wide variety of clinical manifestations, epidemiological exposures, and causative serovars of disease in an endemic region of Japan. We also found that JHR occurs frequently, and its recognition may be important for the diagnosis and management of leptospirosis in the early stage when laboratory confirmation is pending.