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Objective: The objective of this study was to compare proximal, local, and distal muscle morphology in women with and without patellofemoral pain (PFP). Materials and Methods: Proximal, local, and distal muscle thicknesses (MTs) were obtained with B-mode sonography in healthy (control group [CG], n = 20) and PFP (PFP group, n = 20) women. In addition, muscle mass was measured by the sum of the synergistic MTs. Data were analyzed by independent t-test, Mann-Whitney U test, and effect size. Results: PFP women had smaller gluteus medius ( P = .02, d = 0.7), vastus medialis ( P < .01, d = 1.0), and flexor digitorum brevis ( P < .01, d = 1.0) MT and greater gastrocnemius medialis ( P = .04, d = 0.6) MT than CG. Quadriceps muscle mass ( P = .01, d = 0.8) and foot muscle mass ( P = .008, d = 0.9) were smaller, while plantar flexor muscle mass was greater in the PFP group than in CG ( P = .01, d = 0.8). Conclusion: PFP women have proximal, local, and distal MT alterations in comparison with CG, which may explain possible changes in muscle strength and functionality.