Post-implant analysis in permanent implant brachytherapy is an important process that provides a feedback on treatment quality. Random seed movements, edema, and needle related factors contribute to deteriorate dose coverage. For a complete study of these movements, it is important to reconstruct the post-implant seeds clusters but, up to now, this task was only possible via a long and difficult manual process. To facilitate post-implant analysis a simulated annealing algorithm was developed to perform automatic reconstructions. This process is fast (30-60 s on a 1.3 GHz pentium) and has a high level of success, even with up to 5% of seed loss. Tests on 21 clinical cases show that the algorithm yields exactly the same results as manual reconstructions. A realistic simulation tool was used to generate 58 synthetic post-implant data, in which cases the exact configuration was known. Even if some errors were found, pertinent information was extracted. For medium seed density [corresponding to seeds of 0.6 mCi (0.762 U)], 97% of seeds are matched with their correct needle and 89% are matched with their correct planned position. This method provides pertinent information that can be used to understand inhomogenous dose coverage in specific prostate quadrants; to make realistic post-implant simulations or to identify seeds belonging to a needle loaded with different seed types or activity.