Muscle cross-sectional area (CSA) is used as a measure for maximum muscle force. This CSA is commonly determined at one location within the muscle and for one jaw position. The purpose of this study was to establish a method to standardize the analysis of the CSA of the masticatory muscles in vivo, and to compare the CSAs along their entire length for two different jaw positions (opened and closed). The CSAs in the planes perpendicular to the long axes of the masseter, medial, and lateral pterygoid muscles were measured in ten normal young adult subjects by magnetic resonance imaging. Our results showed large differences among the muscles and a non-uniform change in CSA after jaw-opening. The method enables the CSA measurement to be standardized in vivo, and allows for a correct comparison of CSAs in different skull morphologies.