A 0.6 kb DNA fragment has been isolated from a genomic sublibrary of the cestode Echinococcus multilocularis. This DNA-fragment showed a strong hybridization signal to 32PdCTP labeled total DNA prepared from E. multilocularis metacestode material. The fragment was subcloned into the Escherichia coli vector Bluescript BS+ resulting in the recombinant plasmid pAL1. The recombinant parasite DNA probe was labeled by biotinylation and hybridized to Southern blots of resolved EcoRI/PstI digested genomic DNA originating from E. multilocularis, E. granulosus and other helminth species (Taenia hydatigena, T. crassiceps, T. saginata, Mesocestoides corti, Hymenolepis diminuta, Moniezia expansa). The Southern blot hybridization experiments revealed that the DNA probe pAL1 was specific for E. multilocularis and E. granulosus. By comparison of the hybridization banding patterns a clear discrimination between E. multilocularis and E. granulosus was possible at the genome level. Furthermore, pAL1 was used to detect genetic variation within a set of different E. multilocularis isolates which had been experimentally maintained in mice by parasite tissue transplantation.