Between January 2001 and December 2005, 1263 patients suspected of having echinococcosis were screened serologically by indirect haemagglutination assay (IHA). IHA-positive patient sera were then retested by western blot for confirmation and differentiation between Echinococcus granulosus and Echinococcus multilocularis infection. Of 43 sera confirmed as Echinococcus-positive, nine appeared to be specific for alveolar echinococcosis (AE) caused by E. multilocularis. AE-positive serological results corresponded to the clinical and/or imaging findings concerning the patients' liver cysts. The detected incidence of AE was 0.45/10(5) inhabitants, which suggests that clinicians and health authorities in Slovenia should give greater attention to AE in the future.