In France, human AE cases are systematically recorded since the end of the 70s and are managed at the Besançon University Hospital in the FranceEchino National register since 2003. This allowed a retrospective analysis of a subset of 245 patients diagnosed in the region of Franche-Comté and the surrounding departments (French administrative divisions) over the last 30 years in order to detect spatial and temporal trends of alveolar echinococcosis (AE). From 1980 to 2010, no changes in the average incidence could be detected on the regional scale. However, the number of human cases significantly decreased in the Doubs department and coincidently increased in the neighbouring Haute-Saône. Kulldorff's statistics indicate a multi-scale aggregation of human cases in space and time. First the Franche-Comté region appeared to form a significant cluster of higher prevalence compared to the surrounding departments. Within the region, a large and significant cluster of AE prevalence was detected in the Doubs department (mostly on the Jura plateau) in the period 1980-89. It split into two clusters of smaller size in 1990-99. Then clusters faded in 2000-2010 and areas of higher prevalence maintained on the Doubs plateaus and extended to the eastern part of the Haute-Saône and the Jura departments. Moreover, the occupational profile of patients changed over the 30 years of the present study with a large decrease of the 'farmer' category. Fox infection surveys were carried out in 1980-89, 1996-2001 and 2007-2010. They show a clear extension of higher prevalence areas towards the north-west of the traditional highly endemic areas of the Jura mountains. This spatial extension may explain the transition from a clustered distribution to a greater homogeneity of human AE prevalence over the region during the study period. Those results solidly support the idea that important changes in human AE distribution and fox infection have occurred in Franche-Comté since the 80s and may still be ongoing.