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Patellofemoral pain (PFP) has often been attributed to abnormal hip and knee mechanics in females. To date, there have been few investigations of the hip and knee mechanics of males with PFP. The purpose of this study was to compare the lower extremity mechanics and alignment of male runners with PFP with healthy male runners and female runners with PFP. We hypothesized that males with PFP would move with greater varus knee mechanics compared with male controls and compared with females with PFP. Furthermore, it was hypothesized that males with PFP would demonstrate greater varus alignment.A gait and single-leg squat analysis was conducted on each group (18 runners per group). Measurement of each runner’s tibial mechanical axis was also recorded. Motion data were processed using Visual 3D (C-Motion, Bethesda, MD). ANOVAs were used to analyze the data.Males with PFP ran and squatted in greater peak knee adduction and demonstrated greater peak knee external adduction moment compared with healthy male controls. In addition, males with PFP ran and squatted with less peak hip adduction and greater peak knee adduction compared with females with PFP. The static measure of mechanical axis of the tibial was not different between groups. However, a post hoc analysis revealed that males with PFP ran with greater peak tibial segmental adduction.Males with PFP demonstrated different mechanics during running and during a single-leg squat compared with females with PFP and with healthy males. Based upon the results of this study, therapies for PFP may need to be sex specific.