Background The present study aims to assess the epidemiological role of different lymnaeid snails as intermediate hosts of the liver fluke Fasciola hepatica in Belgium and Luxembourg. Methods During summer 2008, 7103 lymnaeid snails were collected from 125 ponds distributed in 5 clusters each including 25 ponds. Each cluster was located in a different biogeographic area of Belgium and Luxembourg. In addition, snails were also collected in sixteen other biotopes considered as temporary wet areas. These snails were identified as Galba truncatula (n = 2474) (the main intermediate host of F. hepatica in Europe) and Radix sp. (n = 4629). Moreover, several biological and non-biological variables were also recorded from the different biotopes. DNA was extracted from each snail collected using Chelex® technique. DNA samples were screened through a multiplex PCR that amplifies lymnaeid internal transcribed spacer 2 gene sequences (500–600 bp) (acting as an internal control) and a 124 bp fragment of repetitive DNA from Fasciola sp. Results Lymnaeid snails were found in 75 biotopes (53.2%). Thirty individuals of G. truncatula (1.31%) and 7 of Radix sp. (0.16%) were found to be positive for Fasciola sp. The seven positive Radix sp. snails all belonged to the species R. balthica (Linnaeus, 1758). Classification and regression tree analysis were performed in order to better understand links and relative importance of the different recorded factors. One of the best explanatory variables for the presence/absence of the different snail species seems to be the geographic location, whereas for the infection status of the snails no obvious relationship was linked to the presence of cattle. Conclusions Epidemiological implications of these findings and particularly the role of R. balthica as an alternative intermediate host in Belgium and Luxembourg were discussed.