Canine inflammatory bowel disease (IBD) is a heterogeneous group of chronic gastrointestinal disorders. The etiology, similar to human IBD, remains unknown. Canine IBD is diagnosed by exclusion, which is a long, time and money-consuming process due to the need of elimination of other diseases presenting with similar symptoms. Therefore, a search for a specific and sensitive marker is needed to overcome these difficulties. The article is divided into 3 sections presenting up-to-date information about laboratory markers, immunohistochemical markers and changes in the neurochemical coding of the enteric nervous system, concentrating on their usefulness and future applications. Data concerning laboratory and immunohistochemical markers is based mainly on canine IBD, while the neuroimmunohistochemistry section presents knowledge from human IBD due to the lack of such studies in veterinary medicine.