We retrospectively studied the clinical and laboratory features and outcomes of chronic enteropathy in Shiba dogs. Among 99 dogs with chronic enteropathy, 21 Shiba dogs (21%) were included in the study (odds ratio, 7.14). No significant differences were seen in signalment, clinical signs, symptoms or laboratory profiles between the Shiba and non-Shiba groups. Severe histopathological lesions in the duodenum were a common finding in the Shiba group. The median overall duration of survival in the Shiba group was 74 days, while that of the dogs in the non-Shiba group could not be determined because more than half of the cases remained alive at the end of this study. The difference between the groups was statistically significant (P<0.0001). The 6-month and 1-year survival rates for the Shiba group were 46% and 31%, respectively. Conversely, the 6-month, 1-year and 3-year survival rates for the non-Shiba group were 83%, 74% and 67%. The results obtained here demonstrated that the Shiba dog is predisposed to chronic enteropathy and shows severe duodenum lesions and poor outcomes, indicating a breed-specific disease.