This study investigated the progressive and regressive phases of bovine papillomavirus (BPV)-1-induced papilloma and fibropapilloma in terms of the distribution of viral antigenicity; E2, E5, and E6 gene activity and expression; and apoptosis (evaluated using DNA in situ fragmentation). All samples from 74 bovine cases of cutaneous lesions with suspected neoplastic changes collected from different skin areas were evaluated. The lesions were diagnosed as papilloma or fibropapilloma using routine hematoxylin–eosin and Mallory’s trichrome staining protocols. Feulgen reactions suggested a possible viral entity, and BPV-1 antigenicity was immunohistochemically observed in 22 cases. E gene expression in neoplastic tissues was evaluated using chromogenic in situ hybridization and reverse-transcription polymerase chain reaction, and the TUNEL method was used to evaluate DNA in situ fragmentation. Differences between progressive and regressive phases in these lesions were analyzed. Ultimately, the number of cases in the progressive phase (18) and regressive phase (4) were determined. Although E2 and E5 gene expression was observed in both phases, E6 gene distribution differed from the other E genes distribution in the progressive phase. E5 gene expression appeared stronger in oncogenic fibrocytes and fibroblasts, whereas E2 and E6 gene expression was weaker in epidermal cells and cells in the regressive phase. Apoptosis, considered the best indicator of neoplastic regression, was found to be associated with the regressive phase but was observed insufficiently in epidermal and dermal samples of the progressive-phase cases. In conclusion, this work provides significant insights on the molecular and immunopathological features of BPV-1.