BACKGROUND: The contribution of lower limb rotational malalignment to patellofemoral pain and instability has been well recognized. The purpose of the present study is to review the role of computed tomography (CT) and magnetic resonance imaging (MRI) in assessment of abnormal rotational alignment of lower limb. EVIDENCE ACQUISITION: An analysis of all available literature in the English language through 2010 was performed to provide data on a comparison between MRI and CT-specifically, the techniques and normative values used to determine abnormal lower limb alignment. RESULTS: CT and MRI are highly accurate in defining abnormal alignment of the lower limb. Determination of axis of femoral anteversion in proximal femur has been the subject of debate in the literature. The determination of distal femoral condylar axis, proximal tibial axis and distal tibial axis are less controversial. CONCLUSIONS: CT and MRI are both used for assessing the rotational abnormalities of the femur and tibia during evaluation for patellofemoral disorders. MRI has an advantage over CT because femoral anteversion measurements are more accurate and ionizing radiation is avoided. A standardized protocol defining the level and axes for measurement of femoral and tibial alignment indices should be used to maintain consistency in measurements.