Mononuclear cell infiltration of the central nervous system and ganglioneuritis are characteristic histopathological findings of proventricular dilatation disease (PDD) caused by parrot bornavirus (PaBV) infection. The purpose of this study was to clarify the link between the degree of inflammatory lesions and the distribution of the virus antigen in naturally PaBV-infected parrots. Pathological examination was performed on 18 PaBV-infected birds identified by reverse transcriptase-PCR. Dilatation of the crop, proventriculus, and ventriculus was observed in all 18 (100%) birds, and dilation of the right ventricle of the heart was observed in 14/18 (78%) birds. Cases were classified based on the scores for the distribution and degree of histological lesions into neural type, with severe brain lesions, digestive type, with severe gastric lesions, or nervous/digestive type, with severe lesions in both the brain and ventriculus. The PaBV immunohistological score correlated with the inflammatory lesion scores. Ganglioneuritis, myocarditis, and myocardial degeneration were frequently observed in the heart. Interestingly, macroscopic and microscopic lesions and virus antigen were detected in the hearts of all three histological types. The present study showed that parrots naturally infected with PaBVs can be grouped into three types based on the lesion distribution, and heart failure is an important symptom in PaBV-infected parrots.