: Patellofemoral pain (PFP) is believed to be a precursor to knee osteoarthritis (OA). The primary purpose of this study was to compare matrix metalloproteinase-9 (MMP-9) levels in young adult females with and without PFP. The secondary purpose was to determine the associations between MMP-9, patella position, hip and knee kinematics, and pain in females with PFP. : Plasma was analyzed for MMP-9. Patellar position was measured using diagnostic ultrasound as the degree of offset (RAB angle) from the deepest aspect of the femoral trochlear groove to the inferior pole of the patella. A positive RAB angle suggested patella lateralization. Hip and knee kinematics during a single-leg squat were measured using 2-dimensional motion analysis and quantified as the dynamic valgus index (DVI), a combined measure of hip and knee motion. A higher DVI suggests increased valgus loading at the patellofemoral joint. Pain was measured using a 10 cm visual analog scale. : Females with PFP had significantly higher levels of MMP-9 than controls (72.7 vs. 58.0 ng/mL, = 0.03). Females with PFP had a significant positive association between MMP-9 and patella lateralization ( = 0.38, = 0.04), suggesting that greater patellar lateralization may contribute to increased joint inflammation. A significant inverse association was observed between MMP-9 and the DVI ( = -0.50, = 0.007), indicating that individuals with higher inflammatory marker levels may adopt movement patterns that reduce valgus loading. : The significant association between MMP-9 and patella lateralization suggested a potential link between patella alignment and joint inflammation, which may contribute to early joint degeneration. The inverse association between MMP-9 levels and the DVI suggested that subjects with higher MMP-9 levels adjusted their movement pattern as a compensatory mechanism to reduce knee valgus stress to reduce joint degeneration.