A slot-scan digital radiography (SSDR) system uses collimated fan beam x-rays synchronized with the movement of a flat-panel detector. This system allows to obtain a full length x-ray image of the body with reduced dose and small image distortion compared with conventional x-ray systems. The purpose of this study was to develop a method for evaluation of the three-dimensional (3D) alignment of the lower extremity using a biplanar SSDR system and bone surface models. The biplanar SSDR system used a rotation table positioned at 0 deg and 60 deg relative to the optical axis of an X-ray source. Camera calibration was performed using an acrylic frame with 72 radiopaque markers. Sawbone femur and tibia were used to replicate the alignment of lower extremity. Three acrylic markers were attached to each sawbone to define the local coordinate system Computed tomography of the sawbone femur and tibia was performed to allow the reconstruction of the 3D surface models. Then the femur and tibia were fixed at three different alignments of the knee; extension, axial rotation, and varus deformity. For each alignment the femur and tibia were imaged using the biplanar SSDR system. The 3D positions of the femur and tibia were recovered using an interactive 2D to 3D image registration method. Overall, the largest estimation errors were 1.1 mm in translation and 0.9 deg in rotation, demonstrating that this method has an adequate accuracy for the clinical usage.