Cytologic examination of exfoliative specimens obtained during endoscopy is a useful and reliable adjunct to mucosal biopsy for the diagnosis of gastrointestinal (GI) tract diseases in dogs and cats. Clinical advantages of endoscopic cytology include simplicity, rapidity of diagnosis and minimal invasiveness. Cytologic smears are graded on the basis of objective criteria, including the presence and number of inflammatory, atypical, and epithelial cells as well as the presence of bacteria, hemorrhage, debris/ingesta, and mucus. There is high correlation between results obtained from endoscopic cytology and histologic examination, and discordant results are infrequent. Brush cytology is useful in detecting mucosal inflammation, whereas touch cytology is more likely to detect acute purulent and erosive mucosal lesions. Alimentary lymphoma my be readily diagnosed using either technique. This article provides an overview of how cytologic smears are prepared and evaluates their diagnostic accuracy.