The Papillomaviridae family comprises a large number of viruses that can infect a broad range of hosts giving rise to benign lesions of the skin or mucosal membranes. Until today, seven viruses termed EcPV1-7 were identified in equine papillomas.Two trotter stallion siblings at the age of two were referred to the Equine Clinic of Free University of Berlin, because of erythema, alopecia and crusting. After a diagnosis of immune-mediated skin disease, the horses underwent long-term treatment with glucocorticoids and azathioprine. Two months later, both horses developed hundreds of small wart-like proliferations on the head, neck, chest and trunk. Six healthy horses, housed in the same stable, were used to assess the occurrence of the virus in healthy skin.Biopsies were obtained for histopathology and for amplification and cloning of the papillomavirus genome as well as for sequence analysis.Histopathology revealed well demarcated cup-shaped epidermal proliferations. Foci were covered by parakeratotic, or abnormally formed, keratin. In deeper layers, numerous enlarged cells with cytoplasmic eosinophilic inclusion-like structures and occasional intranuclear basophilic inclusion bodies were striking, existing beside cells with a peripheral cytoplasmic clearing (koilocytes). Histopathological findings were consistent with endophytic papilloma similar to the Le Net-type described in immunosuppressed dogs caused by a distinct canine papillomavirus. Furthermore, papillomavirus DNA was detected in tissue samples using a broad range PCR analysis. Preliminary phylogenetic analysis of a partial sequence from the L1 gene indicated a putative new papillomavirus that has not been described in horses so far. Biopsies of the control horses showed no abnormalities in histopathology and were tested negative for the putative novel papilloma virus DNA.