Internal and external rotation of the femur plays an important role in defining the orientation of the patellofemoral joint, influencing contact areas, pressures, and cartilage stress distributions. The purpose of this study was to determine the influence of femoral internal and external rotation on stresses in the patellofemoral cartilage. We constructed finite element models of the patellofemoral joint using magnetic resonance (MR) images from 16 volunteers (8 male and 8 female). Subjects performed an upright weight-bearing squat with the knee at 60° of flexion inside an open-MR scanner and in a gait laboratory. Quadriceps muscle forces were estimated for each subject using an electromyographic-driven model and input to a finite element analysis. Hydrostatic and octahedral shear stresses within the cartilage were modeled with the tibiofemoral joint in a “neutral” position and also with the femur rotated internally or externally by 5° increments to ±15°. Cartilage stresses were more sensitive to external rotation of the femur, compared with internal rotation, with large variation across subjects. Peak patellar shear stresses increased more than 10% with 15° of external rotation in 75% of the subjects. Shear stresses were higher in the patellar cartilage compared to the femoral cartilage and patellar cartilage stresses were more sensitive to femoral rotation compared with femoral cartilage stress. Large variation in the cartilage stress response between individuals reflects the complex nature of the extensor mechanism and has clinical relevance when considering treatment strategies designed to reduce cartilage stresses by altering femoral internal and external rotation.