This study used magnetic resonance imaging (MRI) to determine whether changes in patellofemoral alignment occur after initial treatment with the Protonics exercise device. The first scan was obtained before the device was used. After performing a set of exercises with no resistance on the device the device was removed, and a second scan was obtained. The same set of exercises was again performed with resistance on the device set at the appropriate level, and a final scan was obtained with the device removed. An isometric leg press was maintained as each image was obtained to simulate more closely a functional weight-bearing activity. Subjects were 26 women with complaints of patellofemoral pain. The main outcome measures were: patellar tilt angle, bisect offset, and lateral facet angle. Nonparametric repeated measures analysis of variance tests showed no differences between test conditions for any of the three measures of patellofemoral alignment. We conclude that after an initial treatment session using the Protonics system there is no change in patellofemoral alignment as determined by MRI.