Recently, a principal component analysis (PCA) approach has been used to provide insight into running pathomechanics. However, researchers often account for nearly all of the variance from the original data using only the first few, or lower-order principal components (PCs), which are often associated with the most dominant movement patterns. In contrast, intermediate- and higher-order PCs are generally associated with subtle movement patterns and may contain valuable information about between-group variation and specific test conditions. Few investigations have evaluated the utility of intermediate- and higher-order PCs based on observational cross-sectional analyses of different cohorts, and no prior studies have evaluated longitudinal changes in an intervention study. This study was designed to test the utility of intermediate- and higher-order PCs in identifying differences in running patterns between different groups based on three-dimensional bilateral lower-limb kinematics. The results reveal that differences between sex- and age-groups of 128 runners were observed in the lower- and intermediate-order PCs scores (p<0.05) while differences between baseline and following a 6-week muscle strengthening program for 24 runners with patellofemoral pain were observed in the higher-order PCs scores (p<0.05), which exhibited a moderate correlation with self-reported pain scores (r=-0.43; p<0.05).