The etiology of patellofemoral pain is likely related to pathological femoral shape and soft-tissue restraints imbalance. These factors may result in various maltracking patterns in patients with patellofemoral pain. Thus, we hypothesized that femoral shape influences patellofemoral kinematics, but that this influence differs between kinematically unique subgroups of patients with patellofemoral pain. 3D MRIs of 30 knees with patellofemoral pain and maltracking ("maltrackers") and 33 knees of asymptomatic subjects were evaluated, retrospectively. Dynamic MRI was acquired during a flexion-extension task. Maltrackers were divided into two subgroups (nonlateral and lateral maltrackers) based on previously defined kinematic criteria. Nine measures of femoral trochlear shape and two measures of patellar shape were quantified. These measures were correlated with patellofemoral kinematics. Differences were found in femoral shape between the maltracking and asymptomatic cohorts. Femoral shape parameters were associated with patellar kinematics in patients with patellofemoral pain and maltracking, but the correlations were unique across subgroups within this population. The ability to better categorize patients with patellofemoral pain will likely improve treatment by providing a more specific etiology of maltracking in individual patients.