The assessment of regional myocardial perfusion using magnetic resonance (MR) imaging 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 a practical implementation of a real-time interactive MR echo-planar (EPI) myocardial perfusion imaging system and demonstrates an automated approach for motion and deformation tracking of functional myocardial perfusion images.