Bright-field transmission electron microscope (TEM) images of ion milled or focused ion beam (FIB) sections of cortical bone sectioned parallel to the long axis of collagen fibrils display an electron-dense phase in the gap zones of the fibrils, as well as elongated plates (termed mineral lamellae) comprised of apatite crystals, which surround and lie between the fibrils. Energy dispersive X-ray spectroscopy (EDS) and electron energy loss spectroscopy (EELS) studies by others have shown that the material in the gap zones is calcium phosphate. Dark-field (DF) images are capable of revealing the projected position of crystals of apatite in a section of bone. We obtained bright field (BF) images of ion milled sections of bovine femoral cortical bone cut parallel to fibril axes (longitudinal view), and compared them with DF images obtained using the (002) apatite reflection to test a widely held theory that most of the mineral in bone resides in the gap zones. Most apatite crystals which were illuminated in DF images and which projected onto gap zones were extensions of crystals that also project onto adjacent overlap zones. However, in BF images, overlap zones do not appear to contain significant amounts of mineral, implying that the crystals imaged in DF are actually in the interfibrillar matrix but projected onto images of fibrils. However a small number of “free” illuminated crystals did not extend into the overlap zones;​ these could be physically located inside the gap zones. We note that projections of gap zones cover 60% of the area of any longitudinal field of view;​ thus these “free” crystals have a high random probability of appearing to lie on a gap zone, wherever they physically lie in the section. The evidence of this study does not support the notion that most of the mineral of bone consists of crystals in the gap zone. This study leaves uncertain what is the Ca-P containing material present in gap zones;​ a possible candidate material is amorphous calcium phosphate.