Small intestinal histologic abnormalities in celiac disease include atrophy of the intestinal villi, hypertrophy of the crypts and lymphocytic infiltration of intraepithelial spaces and lamina propria. These findings are central to diagnosis and their severity and change over time are valuable to monitor disease course and response to therapy. Subjective methods to grade celiac disease histological severity include the Marsh-Oberhuber and Corazza-Villanacci systems. Quantitative histology uses villus height (Vh), crypt depth (Cd), and intra-epithelial lymphocyte count (per 100 enterocytes) to provide objective measures of histologic changes including Vh:Cd ratio. Here we examine the available literature regarding these methodologies and support the use of quantitative histology as the preferred method for accurately and reproducibly demonstrating change of relevant histologic end points over time. We also propose a Quantitative-Mucosal Algorithmic Rules for Scoring Histology (Q-MARSH) system to partially align quantitative histology results with the traditional Marsh, Marsh-Oberhuber, and Corazza-Villanacci systems. Q-MARSH can provide a standardized, objective, and quantitative histology scoring system for use as a clinical or research application.