Disaccharidase (DS) activity in duodenal biopsy specimens is the gold standard for diagnosing DS deficiency. We investigated strategies to reduce the need for DS testing and whether clinical or histopathologic factors predict DS deficiency. A retrospective chart review analyzed 1,678 DS results in children, biopsy indication(s), and duodenal histopathology. One or more DSs were abnormal in 42.8%. Sufficient lactase predicted sucrase, palatinase, and maltase sufficiency (negative predictive value 97.7%). Three patients had sucrase-isomaltase deficiency (0.2%). DS deficiency was more common in biopsy specimens for positive celiac serology (78.0%). Villous blunting, intraepithelial lymphocytosis, and active inflammation predicted DS deficiency; a combination of any two had an 81.4% positive predictive value. Utilization could be reduced by only testing cases with normal duodenal histopathology and ongoing clinical suspicion for DS deficiency after reviewing pathology. In cases with suspected celiac disease and/or mucosal injury, DS deficiency is common and likely secondary, limiting test utility.