The assessment of regional myocardial perfusion during the first-pass of a contrast agent bolus requires tracking of the signal time course for each myocardial segment so that a detailed perfusion map can be derived. To obtain such a map in practice, however, is not trivial because deformation of the shape of the myocardium and respiratory-induced motion render a major difficulty in this process. This study describes an automated approach for motion and deformation tracking of functional myocardial perfusion images. The effectiveness of the described method has been evaluated using a numerical phantom and results are compared with those from existing techniques which use deformable models. Preliminary results from applying our approach to 20 patients are discussed and compared with those from SPECT studies.