Quantifying joint congruence may help to understand the relationship between joint function and health. In previous studies, a congruence index (CI) has been used to define subject-specific joint congruence. However, the sensitivity of the CI algorithm to surface representation was unknown. The purpose of this study was to assess the effects of applying five modifications (M1–M5) to the CI algorithm to determine whether the magnitude and variability of the patellofemoral CI is dependent on the surface representation used. The five modifications focused on calculating the CI based on the principal curvature (M1) at the centroid of the contact region, (M2) using an root mean square value for the contact region, (M3) using a mean value for the contact region, (M4) using all digitized points of the patellar surface, and (M5) using all digitized points in contact. The CI found using the contact area (M1, M2, M3, and M5) provides a local measure for congruence, which was shown to increase (decreasing CI) with increasing joint angle. In ten healthy subjects measured with magnetic resonance (MR) images, the patellofemoral joint became significantly more congruent as the knee angle increased from 15 deg to 45 deg using method M5. The magnitude and variability of the patellofemoral CI was dependent on the surface representation used, suggesting that standardization of the surface representation is important to provide a consistent measure. Specifically, M5 provides a local measure of joint congruence, which can account for joint position and orientation. M5 balances the ability to detect differences in congruence between knee angles without introducing high variability.