Zoonoses have a different impact on public health, determined by geographical and socio-economic factors, which requires their prioritization for prevention and control purposes to be performed at the national level. Prioritization of zoonoses is a mechanism used in policy-making, primarily in allocating available resources. Aim of the paper is to compare two different methods used for prioritization of zoonoses by Institute of public health (IPH) and Food and Veterinary Agency (FVA). Material and methods: IPH used a method prepared by the U.S. Centers for Disease Control and Prevention (CDC), - One Health Zoonotic Disease Prioritization (OHZDP) tool, adapted to national conditions (2019). FVA used a standardized semi-quantitative method based on the OIE Methodological Manual (List and Categorization of priority diseases in animals including and those transmitted to humans). A total of 21 zoonoses have been selected, based on their importance for the human and veterinary sector. These diseases are ranked according to the stated criteria of the two previously conducted prioritizations and their comparison is performed. Results: With the prioritization conducted by IPH and FVA the first 5 ranked zoonoses are: Hemorrhagic fevers with renal syndrome, Leishmaniasis, Tularemia, Brucellosis and Listeriosis. With the prioritization carried out by the FVA the first 5 ranked zoonoses are: Bovine brucellosis, Bovine tuberculosis, Salmonellosis, Avian influenza and West Nile fever. A Cumulative Annual Incidence is taken as a control parameter. Regarding this, the 5 first ranked zoonoses are Echinococcosis, Brucellosis, Lyme fever, Leishmaniasis and Tularemia. Conclusions: A comparative analysis of the separate lists of priorities for human and veterinary medicine shows that only a certain percentage overlap. Also, the presence of a number of zoonoses with endemic character, but also a more pronounced risk of new emergent diseases, determines the need to provide consensus on the methodology of prioritization of zoonoses, and its formalization and institutionalization, as a crucial step towards identification and prioritization of zoonoses that would be the subject of joint programs and interventions.