We present an algorithm, based on simulated annealing, for automatic seed matching and three-dimensional spatial coordinate reconstruction using either three radiographic films or three fluoroscopic images taken from different perspectives. The matching problem is defined in the framework of combinatorial optimization, which allows robust reconstruction in presence of calibration imprecision, patient movements, and isometric distortions. Furthermore, by using a global criterion to select the correct matching, we evade common problems of the three-film method and its variants in presence of noise. The algorithm has been tested on 112 clinical cases and 100 simulated implants and used clinically on more than 100 cases. Simulated implants were reconstructed with an average error of 0.21 mm. For clinical cases, comparison of the precision is performed between results obtained with this new method and results obtained using the three-film technique. Compared to the latter technique, the reconstruction precision was improved in 62% of the clinical cases.