Repeated acquisitions of computed tomography and magnetic resonance imaging are increasingly used during radiotherapy treatment to accurately deliver radiation while limiting side effects. This is only feasible however after all acquisitions have been correlated to a single reference scan using a deformable registration method. This paper presents a parallel implementation of one such method, the viscous-fluid registration method, on modern graphics hardware. A significant speedup close to two orders of magnitudes was observed when comparing to a CPU based implementation. As a consequence of the reduced registration time it is now feasible to perform larger scale clinical evaluation of the method. An example of registration results obtained during a treatment course is included in the paper.