The purpose of this study is to compare the effect of two types of quadriceps strengthening protocols on morphological characteristics of the knee vastus muscles in patients with lateral patellar compression syndrome. 48 female patients were randomly divided into 3 groups: selective (16), general (17) and control (15). The selective group participated in an isokinetic knee extension training protocol at the last 30° knee extension arc with maximum leg external rotation at high speed with the aim of selectively strengthening the vastus medialis muscle. The general group participated in an exercise protocol aimed at strengthening the entire quadriceps muscle. Both these protocols lasted 8 weeks. The control group did not receive any intervention. The vastus medialis and lateralis muscles cross-sections and fibers angles were measured using an ultrasound device. The data were analyzed using repeated-measures ANOVA and dependent t tests. At pre-intervention, there were no differences between groups in muscles cross-sections and fiber angles (P > 0.05), but after interventions, in selective group, the vastus medialis cross-section and fiber angle, as well as vastus medialis to vastus lateralis cross-section ratio, were significantly higher than other groups (P < 0.01). Also, compared to pre-intervention, the vastus medialis cross-section and fiber angle increased only in selective group (P = 0.001), and the vastus lateralis cross-section increased only in general group (P = 0.001). Use of isokinetic extension exercises targeting selectively strengthening the vastus medialis can improve the activity and involvement of this muscle-which is impaired in chronic patellofemoral joint disorders - by changing its morphology. •Isokinetic knee extension exercise to selectively strengthen vastus medialis significantly increases the muscle fiber angle.•It also significantly increases the vastus medialis cross-section and the ratio of its cross-section to the vastus lateralis. It can improve the vastus medialis function, which is impaired in chronic patellofemoral disorders, by changing its morphology.