Introduction: Patellofemoral pain syndrome is one of the most common muscloskeletal impairment presenting to orthopedia clinics and sports medicine centers that accounted for 57% of all knee problems in runners. it has been reported that patella lateralization and trochlear dysplasia are the most important malalignment factors related to patellofemoral joint (PFJ) that may lead to high compression force on lateral side of knee and finally damaging this joint specially in runners and other athletics. The aim of this study was the comparison of some biomechanical parameters including the patella deviation and Sulcus angle between two groups of healthy and patellofemoral pain syndrome (PFPS) patients by using noninvasive and precise methods of MRI. Methodology: 21 subjects in range of 50-20 ages were classified into two groups of healthy (n=10) and patients with PFPS (P=11). MRI imaging was done for subject’s knee in 40 degree flexion. Patella deviation were measured by angle congruence. Results: patella lateralization average in healthy group was 1.3±8.5 and in PFPS group was 7.6±9.10 that was 86% higher in patient group than healthy one and this difference was significant statistically (p=0.04), while there was no significant difference in the Sulcus angle. Discussion: findings shows that the cause of pain due to patella lateralization could not relate to shallowing the trochlear groove but may result of muscles weakness. Due to ability of muscles to control of patella lateralization, delaying or weakness of Vastus Medialis Oblique (VMO) can be a risk factor for inappropriate displacement of patella. As a result of patellofemoral joint malalignment,undesirable and excessive tensions and also shearing force are created that more than the threshold of physiological tissue and can lead to cartilage damage, degenerative changes, ligamentous structures strain and patella laterallization and can cause pain in a wide range of activities in patients with patellofemoral pain