Congenital diseases of the large intestine have scarcely been reported and mostly include fistula, atresia, or colonic duplication. Cases of partial colonic agenesis have rarely been described. The purpose of this study was to report a cohort of dogs and cats diagnosed with partial colonic agenesis. The colon was measured during colonoscopy or contrast-radiography and compared to the average length described in the literature. Six dogs and 17 cats were retrospectively included. Depending on the case, partial colonic agenesis could represent an incidental finding or the likeliest cause of clinical signs. Diarrhea was reported in most cases, and no specific clinical or biological abnormality was observed. Median age of presentation was variable and long asymptomatic periods were common. Abdominal ultrasound was useful and identified a short colon in 14/17 cats but only in one dog. Endoscopy was useful to confirm the diagnosis and to identify associated lesions and complications. Among others, colonic stenosis was reported in 8/9 cases that had lifelong clinical signs and the shortest colon length. This anatomical abnormality could promote chronic inflammation that might generate fibrosis and ultimately stenosis.