A new method has been developed for analyzing transmural distributions of finite deformation in canine ventricular myocardium without the need to assume that the strain in a finite volume of the wall is homogeneous. The three-dimensional nodal geometric parameters of bilinear-cubic or bilinear-quadratic finite elements are fitted by least squares to the measured coordinates of 12-18 radiopaque markers implanted in the left ventricular free wall. For six dog hearts, root-mean-squared errors in the fitted in-plane coordinates ranged from 0.079-0.556 mm in the end-diastolic reference state and 0.142-0.622 mm at end-systole. The corresponding error ranges in the radial coordinate were 0.042-0.264 mm at end-diastole and 0.106-0.279 mm at end-systole. Smoothly continuous transmural profiles of wall strain computed as the element deformed during the cardiac cycle from end-diastole to end-systole showed good agreement with the discrete results of conventional homogeneous analysis. Using the kinematics of a thick-walled incompressible cylinder, overall absolute errors due to the non-homogeneity of myocardial deformation were found to be reduced in the new analysis by 30-35% for typical experimental parameters. Overall relative errors were also reduced (from 23 to 20%). Since measurement errors in the reconstructed marker coordinates were spatially smoothed by the fitting procedure, noise in the computed deformations was also substantially attenuated, and transmural gradients of three-dimensional strain components could be obtained with improved accuracy. Hence physiological factors affected by transmural stress and strain distributions, such as myocardial blood flow, ischemia and hypertrophy, may be better understood.