Patellofemoral pain syndrome (PFPS) remains a prevalent athletic injury, especially among females. Hip strength differences between females with and without PFPS has led to speculation that individuals with PFPS are prone to abnormal lower extremity alignment during weightbearing activities. This is thought to be due, in part, to an inability to adequately resist external moments at the hip. This tendency for malalignment may be especially evident if weightbearing activities are performed in a state of fatigue. The first aim of this study was to analyze lower extremity mechanics in females with and without patellofemoral pain (PFPS) during three different activities. We hypothesized that differences in lower extremity mechanics between groups would increase during activities with greater loading. 20 females with PFPS and 20 healthy female controls performed single leg (SL) squats, running, and repetitive SL jumps. The results suggest the PFPS group consistently demonstrates altered lower extremity kinematics during each activity, regardless of the magnitude of the external load. For the second aim, we examined the effect of exertion on hip strength and lower extremity mechanics between groups during SL jumps. We hypothesized that differences between groups would be greater following the exertion protocol. However, PFPS subjects demonstrated hip mechanics that differed from the control group throughout the protocol, and both groups demonstrated a similar response to exertion. The third aim of this study was to examine the association between trunk, hip, and knee joint strength and lower extremity mechanics between groups. Subjects with PFPS exhibited decreased hip and trunk strength compared with healthy subjects. However, these strength measurements were weakly to moderately correlated with mechanics suspected to contribute to the etiology or exacerbation of PFPS. The final aim of this study was to evaluate the construct validity and clinical utility of a 2D measure of lower extremity alignment (FPPA). The results suggest that the FPPA may be a useful clinical measure. The FPPA was significantly associated with LE kinematics known to increase retropatellar stress during dynamic activities. Additionally, PFPS subjects demonstrated greater FPPA values than the control group. The results of these four aims highlight kinematic and kinetic differences between females with and without PFPS which may contribute to the exacerbation and etiology of this condition. Conservative treatment programs focused on minimizing these differences in hip strength and lower extremity mechanics may improve long term patient outcomes.