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To develop a 3D MR tagging method that combines harmonic phase (HARP) and homogeneous strain analysis methods for quantification of regional myocardial wall motion in mice.3D tagged images were acquired from seven C57BL/6 mice. Intersecting tag points were reconstructed and 3D strains were quantified at apical, midventricular, and basal levels. Circumferential and radial strains quantified with 2D MR tagging were compared with those calculated from 3D tagged images.Our data showed significant heterogeneity in radial, circumferential, and shear strains. Longitudinal strain was more homogeneous. The circumferential-longitudinal shear strain, a unitless measure of ventricular torsion, was positive throughout the left ventricle. There were strong correlations between 2D and 3D studies at the basal and midventricular levels.This work demonstrates the feasibility of 3D characterization of cardiac function in mouse via the combination of HARP and homogeneous strain analysis. J. Magn. Reson. Imaging 2008;27:1263–1270. © 2008 Wiley-Liss, Inc.