Background: To manage patellofemoral joint disorders, a complete understanding of the in vivo patellofemoral kinematics is critical. However, as one of the parameters of joint kinematics, the location and orientation of patellofemoral finite helical axis (FHA) remains unclear. The purpose of this study is to quantify the location and orientation of the patellar FHA both in vivo and non-invasively at various flexion angles and to relate the FHA to the trans-epicondyle axis (TEA).Methods: The Magnetic resonance (MR) images of 18 unilateral knees were collected at full extension and at 30°, 60°, 90°, and maximum angle of knee flexion. Three-dimensional models of knee joint at different flexion angles were developed with the MR images, and were used to calculate the patellar tracking and FHA with a spline interpolation algorithm. By using a coordinate system based on the TEA, the FHA tracking was quantified. Six parameters concerning the location and orientation of the patellar FHA were analyzed.Results: The average patellar FHA of 18 knees drew an L-shaped tracking on the midsagittal plane moving from the posteroinferior side of the TEA to the anterosuperior with knee flexion. Before 90° flexion, the patellar rotational radius decreased slightly, with an average value of 5.65 ± 1.09 cm. During 20° to 90° knee flexion, the average angle between the patellar FHA and TEA was approximately 10° and that between the FHA and coronal plane was maintained at about 0°, while that between the FHA and level plane fluctuated between -10° and 10°.Conclusions: Patellar FHA was not fixed during flexion, which showed a close relationship with femoral TEA in both location and orientation. The results could help us better understand the patellofemoral joint kinematics and further deal with troublesome patellofemoral disorders.