In France, haemorrhagic fever with renal syndrome (HFRS) is endemic along the Belgian border. However, this rodent-borne zoonosis caused by the Puumala virus has recently spread south to the Franche-Comté region. We investigated the space–time distribution of HFRS and evaluated the influence of environmental factors that drive the hantavirus reservoir abundance and/or the disease transmission in this area. A scan test clearly indicated space–time clustering, highlighting a single-year (2005) epidemic in the southern part of the region, preceded by a heat-wave 2 years earlier. A Bayesian regression approach showed an association between a variable reflecting biomass (normalized difference vegetation index) and HFRS incidence. The reasons why HFRS cases recently emerged remain largely unknown, and climate parameters alone do not reliably predict outbreaks. Concerted efforts that combine reservoir monitoring, surveillance, and investigation of human cases are warranted to better understand the epidemiological patterns of HFRS in this area.