This thesis deals with the molecular diagnosis of infectious diseases concerning animal and human health: in particular, with diseases notifiable to the World Organization for Animal Health, OIE (the vesicular complex and avian influenza), as well as with Hepatitis E, representing emerging zoonotic aspects. With the worldwide introduction and use of the polymerase chain reaction (PCR) methodologies, the detection of different pathogens improved significantly - however, these systems have weak points as well. The parallel screening of more than a few pathogens is not resolved and, in general, the multiplexing capacity of most of the methods used in this area is insufficient. In the case of the detection of pathogens causing similar symptoms (like the vesicular complex, involving Foot-and-Mouth Disease (FMD), Swine Vesicular Disease (SVD) and Vesicular Stomatitis (VS), the immediate differential diagnosis is essential, not only regarding the multiplexing, but also because of the high economic risks and the strict legislations. Subtyping of the avian influenza viruses is a broad and extensive task because it needs to differentiate 16 hemagglutinin and 9 neuraminidase types and their variants. The padlock probes, as used in these studies, seem to be optimal to fulfill the multiplexing requirements and to provide novel, high-throughput tools for the improved diagnosis of the vesicular complex and of avian influenza. The general detection and subtyping of Hepatitis E Virus (HEV) is an important and complicated task today, as the virus shows zoonotic potential by causing endemics in humans and persisting infections in different animal species. Thus, there is a high need for sensitive and specific methods and identification of HEV variants. In the frame of this work, a highly specific and sensitive diagnostic assay was developed, based on two types of real-time PCR methods. In addition, a genotyping system was constructed using a simple and quick ligation-based technique
