Abstract Background Contrast-enhanced ultrasonography (CEUS) can be used to evaluate intestinal perfusion in healthy dogs. It is helpful for diagnosing and monitoring inflammatory bowel disease in humans and could be useful for dogs with chronic intestinal diseases. Objectives To examine duodenal perfusion in dogs with chronic inflammatory enteropathy (CIE) and intestinal lymphoma. Animals Client-owned dogs with CIE (n = 26) or intestinal lymphoma (n = 7) and dogs with gastrointestinal signs but histopathologically normal duodenum (controls, n = 14). Methods In this cross-sectional study, dogs with CIE were classified into remission (n = 16) and symptomatic (n = 10) groups based on clinical scores determined at the time of CEUS. The duodenum was scanned after IV injection of Sonazoid® (0.01 mL/kg). CEUS-derived perfusion parameters, including time-to-peak, peak intensity (PI), area under the curve (AUC), and wash-in and wash-out rates were evaluated. Results The PI was significantly higher in the symptomatic CIE group (median (range); 105.4 (89.3-128.8) MPV) than in the control group (89.9 (68.5-112.2) MPV). The AUC was significantly higher in the symptomatic CIE group (4847.9 (3824.3-8462.8) MPV.sec) than in the control (3448.9 (1559.5-4736.9) MPV.sec) and remission CIE (3862.3 (2094.5-6899.0) MPV.sec) groups. The PI and clinical score were positively correlated in the CIE group. No significant differences in perfusion parameters were detected between the lymphoma and CIE groups or the lymphoma and control groups. Conclusions and Clinical Importance The PI and AUC can detect duodenal inflammation and hence are potentially useful for excluding a diagnosis of CIE.