In the past years, the diagnostic tools applied to identify alveolar (AE) and cystic echinococcosis (CE) in human patients have not only increased in number but also substantially improved in quality. The identification and characterization of species-specific parasite proteins/antigens allowed to generate subsequently recombinant or synthetic polypeptide antigens, as well as corresponding monoclonal antibodies. Some of these new tools have already demonstrated operating characteristics superior to conventional tests used for the immunodiagnosis of CE and AE, and thus may be suggested for routine laboratory application. Powerful molecular techniques, such as the polymerase chain reaction (PCR), have been developed and adapted to advance laboratory diagnosis of AE and CE. Detecting minute amounts of parasite DNA and mRNA, not only to identify but also to characterize the biological status of parasite material, thus becomes a complementary method to synergize immunodiagnostic techniques. This review focuses on recent developments of molecular tools, discussing their potential use as a primary or a supporting diagnostic element. We also outline some future developments to be undertaken in the field of molecular diagnosis, linked to clinical and laboratory problems.