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Haemorrhagic fever with renal syndrome (HFRS) is a type of vector-borne zoonosis sensitive to climate change. To explore the short-term effect of air temperature and amount of precipitation on HFRS incidence, a total of 13722 clinically confirmed HFRS cases from January 1977 to December 2001 in Junan County, China were included in this study. According to symmetric bidirectional case-crossover design, the hazard period (the three calendar months preceding the month when the case was diagnosed) and the control period (the same calendar month of the year before and the year after the hazard period) matched and conditional logistic regression was used to examine the effect of monthly mean temperature and precipitation on the risk of HFRS. The results showed the facilitating climatic conditions for HFRS included: condition with moderate mean air temperature (10–25 °C) and abundant precipitation (> 120 mm) 3 months before [odds ratio (OR) 1·346, 95% confidence interval (CI) 1·191–1·522] and 2 months before (OR 1·193, 95% CI 1·063–1·339); and condition with temperature >25 °C and abundant precipitation (> 120 mm) 3 months before (OR 1·17, 95% CI 1·004–1·363). Temperature of 10–25 °C and moderate precipitation (10–120 mm) in the current month was the most favourable condition for HFRS incidence.