The role of Papillomaviruses (PVs) in the development of canine cancers is controversial. However, recently a novel canine PV (CPV3) was detected in a dog affected with a condition reminiscent of Epidermodysplasia Verruciformis (EV). The aim of the present study was to investigate into the seroprevalence of CPV3 by using generic ELISAs for the detection of antibodies against either canine oral papilloma virus (COPV) or CPV3. Therefore, the capsid proteins of both PV types were expressed as GST-fusion protein antigens and adsorbed to glutathione casein-coated ELISA plates. After showing that PV type-specific antibodies could be detected in the sera from dogs with confirmed COPV or CPV3 infection, CPV3- as well as COPV-seropositive dogs were detected in two sets of canine sera collected in Switzerland and South Africa, respectively. We found specific antibodies against COPV as well as against CPV3 among the tested sera and also a large number being positive for both antigens. The seroprevalence for PV antibodies was hereby with 21.9% (COPV) and 26.9% (CPV3) among the tested dogs from South Africa higher than among the dogs from Switzerland with 10.5% (COPV) and 1.3% (CPV3). Our data suggest a need for further CPV-related seroepidemiological surveys in different countries, especially in the context of clinical manifestations and possible breed predispositions. For this purpose, the newly developed ELISAs can be a useful tool.