Individuals who undergo anterior cruciate ligament reconstruction are at elevated risk for developing early-onset patellofemoral joint osteoarthritis. Our objective was to use K-means clustering to ascertain whether individuals at risk for patellofemoral joint osteoarthritis could be identified as determined by the presence of multiple co-existing anatomical and patella alignment risk factors. Forty participants (20 after anterior cruciate ligament reconstruction, 20 healthy controls) underwent magnetic resonance imaging assessment of the patellofemoral joint. Measures of hypothesized risk factors for patellofemoral joint osteoarthritis were obtained including patella alignment (lateral patella displacement and tilt), trochlear morphology (sulcus angle, lateral inclination angle), patella height (Insall-Salvati ratio and patella articulating overlap), and patellofemoral joint contact area. K-means clustering (k = 2) was used to ascertain whether a high-risk group could be identified. Following clustering, two distinct groups were detected. Participants assigned to cluster 1 exhibited features consistent with patellofemoral joint osteoarthritis including greater lateral patellar displacement and tilt, flatter trochlear grooves and lower lateral trochlear inclination, less patella articulating overlap, and reduced contact area. The proportion of females after anterior cruciate ligament reconstruction assigned to cluster 1 was 75% (N = 15) compared to 25% of healthy females (N = 5). K-means clustering was capable of characterizing individuals at elevated risk for patellofemoral joint osteoarthritis based on the presence of multiple co-existing anatomical and patella alignment risk factors. The fact that a significant percentage of females were assigned to the high-risk cluster supports the clinical observation that these individuals may be at higher risk of early-onset patellofemoral joint osteoarthritis.