Gastrointestinal endoscopy is a minimally invasive diagnostic tool for cats and dogs with signs of gastrointestinal disease. This retrospective study examined the case records of six cats and one dog diagnosed with perforation secondary to gastrointestinal endoscopy. Gastrointestinal perforation occurred in 1.6% of cats and 0.1% of dogs that underwent endoscopy during the 17 yr study period (from 1993 to 2010). It can be difficult to predict what animals are at risk for gastrointestinal perforation but possible risk factors suggested by this study include small intestinal infiltrative disease in cats and preexisting gastrointestinal ulceration in both cats and dogs. Overall, gastrointestinal endoscopy is associated with a low rate of gastrointestinal perforation.