Inflammatory bowel disease (IBD) in dogs is often characterized by a relapsing and remitting clinical course. Determination of inflammatory activity is important for assessing the disease extent, severity, and tailoring appropriate treatment. The study was conducted to record the macroscopic and microscopic changes associated with IBD to assess the usefulness of endoscopy in the diagnosis of the disease and to correlate the clinical activity index (CIBDAI) with endoscopic score. Thirty-three dogs with idiopathic IBD were selected after thorough examination and exclusion. Gastroduodenoscopy and colonoscopy were performed to document the gross macroscopic intestinal lesions. Histopathology of endoscopic aided biopsy samples was used to confirm the disease. Mucosal erythema and increased friability were the most predominant endoscopic findings in the stomach, duodenum, and colon of IBD dogs. Lymphoplasmacytic infiltration was predominant in the mucosal samples on histopathology and diffuse form of IBD is more common in canines. Gastroduodenoscopy and colonoscopy in combination with endoscopically guided biopsy and histopathology are of value in the assessment and diagnosis of IBD. There was no correlation between the clinical inflammatory bowel disease activity index (CIBDAI) with the endoscopic score. A diffuse form of IBD and colitis is more common in dogs in comparison to human IBD where the disease manifests in two distinct forms. Colonoscopy with ileal biopsy could act as a gold standard in the confirmation of diffuse IBD in dogs. CIBDAI can be used as a reliable measure of clinical signs of inflammation and histopathology can be used as a definitive diagnosis of intestinal inflammation.