Patient positioning accuracy can be quantified by the three-dimensional (3-D) translations and rotations required to transform the patient back to the desired position. Results of the current study show that the translations and rotations could be obtained from two projection images obtained radiographically on a linear accelerator when spherical radio-opaque markers were implanted inside or affixed to the surface of a skull phantom. In this study, film used to record the images were converted into digital gray scale images using a laser film digitizer. The marker images were located automatically by the computer using image processing techniques. By combining information from both projections, the 3-D locations of the markers were determined to submillimeter precision. Pairs of films were also analyzed for the phantom displaced from its original location by known amounts. The accuracy of the computed translations and rotations required for realignment of the phantom were found to be better than 1 mm and 0.3 degrees, respectively; comparable to the accuracy of the readout system of the equipment used. The general methodology could be coupled with an electronic portal imaging device for use in computer aided or automated correction of patient position in radiotherapy.