Previous basic bone studies in cranial bone biology and bone grafting have used calipers, volume displacement, and cephalometric tracings to measure membranous bone and to infer fundamental properties of cranial bone. These tools have limited accuracy and reproducibility. Histomorphometry has also been used in the quantitative analysis of cranial bone; however, two-dimensional histology is unable to capture a precise representation of the three-dimensional structure of bone. For the first time, we have used the advanced technology of three-dimensional microcomputed tomographic (micro-CT) scanning as a highly accurate and automated tool to precisely measure changes in bone stereology, volume and projection, and microarchitecture in the evaluation of membranous bone. The advantages of this technology are numerous and include the rapid and nondestructive three-dimensional analysis of bone microstructure at resolutions between 10 and 75 microns. Measures of "connectivity" in three dimensions and the architectural parameter of "anisotropy" are available through micro-CT imaging but can only be inferred through two-dimensional histological series. We successfully imaged two full-thickness cranial bone specimens and one cancellous iliac bone graft. The images demonstrate a similarity between the two membranous specimens and a marked difference in comparison with the endochondral graft. These differences are borne out by mathematical analysis, and their significance is discussed. The utility of micro-CT in the evaluation of membranous bone was displayed by its ability to rapidly calculate differences in bone stereology and to quantitatively measure morphological changes at an ultrastructural level. We believe the benefits of this system will prove to be extremely useful for investigations into the basic biology of membranous bone, bone grafts, and craniofacial interfaces, and we encourage its use by other scientific investigators in the field of craniofacial surgery as they strive for more scientifically rigorous tools to understand the basic biology of membranous bone.