Contagious ectyma is a disease caused by Orf virus, a member of the family Poxviridae, genus Parapoxvirus. In the doctoral dissertation, we describe the analysis of two genomes of Orf virus isolates in chamois (strain ORFV_82/13 and strain ORFV_12/17). Using next-generation sequencing (NGS), we were the first ones to identify nearly complete genome of Orf viruses in chamois. The analyses revealed a high degree of similarity to Orf virus found in sheep and goats. At the nucleotide sequence level, the genomes are 99.93 % identical to each other and differ from other Orf viruses from 7.61 % (sheep strain NZ2) to 11.62 % (goat strain NP). Phylogenetic analysis of genes in the central region has shown that chamois Orf viruses form a distinct phylogenetic group. In the doctoral dissertation, the presence of antibodies against Orf viruses by serum neutralization assay was used to determine the seroprevalence of chamois population with Orf virus. Forty serum samples from chamois were tested. Test results were negative for 38 samples, and two results could not be read due to the cytotoxic effect of the serum sample on the cell culture. By reviewing the archival samples of the last two decades, considering the data provided by hunting organisations and the experience of the Institute of Pathology, wild animals, fish and bees, we found cyclic occurrence of contagious ecthyma in chamois. Fibropapillomas are benign skin tumours caused by viruses of the Papillomaviridae family. The disease with pronounced clinical signs shows a tendency to spread among the roe deer population in Europe, whereas it is rarely observed in red deer. The dissertation describes cases of fibropapillomatosis in roe deer and red deer with a characteristic clinical and histopathological picture. NGS method was used to determine the nucleotide sequence of the whole genome of seven papillomaviruses (PV), namely the sixth PV strain in roe deer (CcaPV1 strain 31-16, CcaPV1 strain 32-16, CcaPV1 strain 37-14, CcaPV1 strain 63-15, CcaPV1 strain 103-16 and CcaPV1 strain 84-14) and one PV strain in red deer (CePV1v strain 64-14). Infections with the CcaPV1 type were confirmed in roe deer and with the CePV1v subtype in red deer. Comparison of the viral genomes with previously known genomes from NCBI GenBank showed high genetic stability of the genome in time and space. Reviewing archival samples from the last two decades, it was found that fibropapillomatosis occurs annually in roe deer but extremely rarely in red deer.