Magnetic resonance (MR) cine images are often used to clinically assess left ventricular cardiac function. In a typical study, multiple 2-D long axis (LA) and short axis (SA) cine images are acquired, each in a different breath-hold. Differences in lung volume during breath-hold and overall patient motion distort spatial alignment of the images thus complicating spatial integration of all image data in three dimensions. We present a fully automatic postprocessing approach to correct these slice misalignments. The approach is based on the constrained optimization of the intensity similarity of intersecting image lines after the automatic definition of a region of interest. It uses all views and all time frames simultaneously. Our method models both in-plane and out-of-plane translations and full 3-D rotations, can be applied retrospectively and does not require a cardiac wall segmentation. The method was validated on both healthy volunteer and patient data with simulated misalignments, as well as on clinical multibreath-hold patient data. For the simulated data, subpixel accuracy could be obtained using translational correction. The possibilities and limitations of rotational correction were investigated and discussed. For the clinical multibreath-hold patient data sets, the median discrepancy between manual SA and LA contours was reduced from 2.83 to 1.33 mm using the proposed correction method. We have also shown the usefulness of the correction method for functional analysis on clinical image data. The same clinical multibreath-hold data sets were resegmented after positional correction, taking newly available complementary information of intersecting slices into account, further reducing the median discrepancy to 0.43 mm. This is due to the integration of the 2-D slice information into 3-D space.