The present study compares the repeatability of patellofemoral malalignment (PFM) indices obtained by 20 degree flexion axial radiography (AR) and computerized tomography (CT) with 0 degree and 20 degree flexion of the knees in children and adolescents. Thirty-one patients with a mean age of 14.2 years (range 8 to 19.2 years) suffering from PFM were examined using these two radiographic techniques. The lateral patellofemoral angle (LPA), the lateral patellar tilt (LPT), and the lateral patellar displacement (LPD) were measured by by two different investigators on different occasions, and the agreement of these indices between CT and AR was evaluated according to Bland and Altman's statistical method. LPT and LPD obtained by AR were more reliable and repeatable than those obtained by CT. The quadriceps muscle contraction exacerbates PFM indices significantly with the knees in full extension (P = 0.0001). LPT and LPD measured at 20 degrees AR show reliably the two pathological components (the patellar tilt and the lateral patellar displacement) of PFM which are necessary for diagnosis and treatment planning. CT with quadriceps contractions is better in qualitative screening of more subtle cases of PFM.