Information about prevalence and breed predisposition of canine chronic enteropathy (CE) is limited. The aim of this retrospective study was to investigate period prevalence, breed disposition, clinical features, diagnostic results, and treatment response of CE in dogs presenting at two Swedish animal hospitals during 2013−2018. A medical record search was performed to identify CE dogs including those with ≥3 visits because of gastrointestinal disease and/or that had undergone gastroduodenoscopy/colonoscopy during 2013−2018. Dog characteristics, case history, physical examination, laboratory variables, therapeutic protocol, and treatment response were recorded. Inclusion criteria for CE were met by 814 dogs. Period prevalence of CE was 1.1% of total number of dogs. Breeds with the highest relative risk included Norwegian Lundehund, West Highland White Terrier, and Miniature Poodle. Median age at presentation was 3.8 (IQR 1.8−6.8) years. French Bulldogs and Miniature Schnauzers presented at a younger age (<2.5 years) compared to other breeds (p < 0.05). In a subset of dogs, serum hypoalbuminemia (116/662, 17.5%), hypocobalaminemia (98/647, 15.1%), and increased C-reactive protein (CRP) concentrations (145/267, 54.3%) were diagnosed. Treatment outcome was classified in 72.9% of dogs and characterized as immunosuppressant-responsive (55.2%), food-responsive (11.4%), non-responsive (5.2%), and antibiotic-responsive (1.1%). Non-responsive dogs were more likely to present with anemia hypoproteinemia/albuminemia, increased CRP, and ascites (p < 0.05). In conclusion, the prevalence of dogs with CE at Swedish hospitals agreed with earlier reports, but risk breeds differed slightly and, compared to other breeds, a younger age of CE onset was found in two breeds. The largest proportion of dogs was immunosuppressant-responsive and the smallest antibiotic-responsive.