Inflammation leads to intestinal dysmotility which can be due to both functional and trophic alterations of the neuromuscular apparatus. To discriminate between trophic and functional changes, several normalization procedures are used in contractility studies. It is important to know how normalization procedures may influence the obtained results. In a rat model of TNBS-induced ileitis, we compared seven known normalization procedures for pharmacological contractions of longitudinal muscle strips. During acute ileitis, contractility was significantly decreased, irrespective of the normalization procedure used. During the post-inflammation phase, hypertrophy and hyperplasia of smooth muscle cells led to increased contractility on raw strip chart recordings. However, when contractions were corrected for the increase in muscle mass, the contractility was either normal or decreased, depending on the normalization procedure used. Normalization of contractions to the cross-sectional area (CSA) of the longitudinal muscle is the gold standard. Comparison of three methods to determine the CSA, showed that the commonly used equation to calculate the CSA, based on the tissue weight, length and density, might overestimate the CSA. We conclude that this equation should be adapted by a muscle thickness ratio, or alternatively the CSA can be determined on histological sections.