Cryptosporidium sp. is a protozoal parasite that can cause hypertrophic gastritis, regurgitation, and chronic wasting in snakes. Diagnosis can be challenging because of intermittent shedding of the organism in the feces. The purpose of this study was to evaluate gastroscopic biopsy as a diagnostic method for Cryptosporidium sp. screening during an outbreak at the Oklahoma City Zoo. Twenty-two snakes were immobilized by chamber induction with an inhalant anesthetic. Gross lesions were seen in seven snakes and consisted of hyperemia, thickening of the gastric mucosa as observed by lack of rugal folds, and a cobblestoned appearance. Gastric biopsy was performed for histologic evaluation (n = 21). Hypertrophic gastritis with intralesional cryptosporidia was diagnosed in five animals. Eleven animals died or were euthanized and complete necropsy was used to evaluate diagnostic measurements of performance of gastric biopsy. Sensitivity for gastric biopsy was 71.4% and specificity was 100%. Gastroscopy appears to be a useful diagnostic method for Cryptosporidium infection in snakes and can help distinguish true infection from prey-based cryptosporidia seen in fecal samples.