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To design a method suitable for obtaining tissue samples from regions of different function as ascertained by magnetic resonance imaging (MRI).In vivo MRI was used to create azimuthal projections of the heart from dilated cardiomyopathy transplant patients with the cardiac valves in the center and four concentric rings representing the septum and free wall. Tagged MRI could identify regions of different contractile strength that were then transferred onto the map projection. The resulting tissue sampling map was used to guide dissection of tissue samples from the explanted heart for analysis by electron microscopy (EM) as well as provide samples for subsequent mRNA analysis. Accuracy of the sampling was determined in a sheep heart using 17 fiduciary markers glued to the epicardial surface.Tagged MRI identified areas of “normal” (%Sc −11), “poor” (%Sc −4) and “failed” contraction (%Sc +3). The mapping method we developed enabled straightforward sampling of these regions after surgical excision. EM showed good tissue preservation while the test of accuracy using the fiduciary markers showed a sampling accuracy of 0.3 ± 3.7 mm. This was similar to the resolution of tagged MRI images themselves.The methods we have developed can accurately guide tissue sampling for ex vivo tissue analysis. J. Magn. Reson. Imaging 2011. © 2011 Wiley Periodicals, Inc.