The accurate delivery of external beam radiation therapy is often facilitated through the implantation of radio-opaque fiducial markers (gold seeds). Before the delivery of each treatment fraction, seed positions can be determined via low dose volumetric imaging. By registering these seed locations with the corresponding locations in the previously acquired treatment planning computed tomographic (CT) scan, it is possible to adjust the patient position so that seed displacement is accommodated. The authors present an unsupervised automatic algorithm that identifies seeds in both planning and pretreatment images and subsequently determines a rigid geometric transformation between the two sets. The algorithm is applied to the imaging series of ten prostate cancer patients. Each test series is comprised of a single multislice planning CT and multiple megavoltage conebeam (MVCB) images. Each MVCB dataset is obtained immediately prior to a subsequent treatment session. Seed locations were determined to within 1 mm with an accuracy of 97±6.1% for datasets obtained by application of a mean imaging dose of 3.5 cGy per study. False positives occurred in three separate instances, but only when datasets were obtained at imaging doses too low to enable fiducial resolution by a human operator, or when the prostate gland had undergone large displacement or significant deformation. The registration procedure requires under nine seconds of computation time on a typical contemporary computer workstation.