Computed tomographic colonography is a minimally invasive technique for detecting colorectal polyps and colon cancer. Most computed tomographic colonography protocols acquire both prone and supine images to improve the visualization of the lumen wall, reduce false-positives, and improve sensitivity. Comparisons between the prone and supine images can be improved by registration between the scans. In this paper, we propose registering colon lumens, segmented from prone and supine images, using feature matching of the colon centerline and nonrigid registration of the lumen shapes represented as distance functions. Experimental registration results (n = 21 subjects) show a correspondence accuracy of 13.77 +/- 6.20 mm for a range of polyp sizes. The overlap in the registered lumen segmentations show an average Jaccard similarity coefficient of 0.915 +/- 0.07.