The diagnosis of hard tissues is generally carried out by bone mineral density (BMD) measurement as a bone quantity parameter. BMD, however, does not necessarily explain bone fracture risks in some clinical cases. Recently, various parameters relating to bone strength have been investigated. These additional parameters, so-called bone quality, reflect intrinsic bone conditions. We have been studying the preferential alignment of the biological apatite (BAp) c-axis among various bone quality parameters. BAp, a dominant component of hard tissue, is an ionic crystal that crystallizes in a hexagonal lattice accompanied with the anisotropic property. In this article, we investigated the osteoclast role in the recovery process of BAp orientation during bone regeneration using osteopetrotic (op/op) mice in which the number of osteoclasts decreases. A surgically drilled, 500-μm diameter hole on each tibia of both control and op/op 8-week-old mice was introduced from the medial surface into the medullary cavity located at a 30% length from the proximal tibia end. After surgery, tibiae injuries were regularly observed by in situ micro-CT, and then the mice were sacrificed four to eight weeks after surgery. BAp orientation was analyzed in and near the regenerated portion by the microbeam X-ray diffraction system. As a result, we found the insufficient recovery of BAp orientation in spite of the apparent repair of bone appearance and quantity from CT images, even eight weeks after surgery in both cases of control and op/op mice. We conclude that this defective animal model can be used to evaluate bone quantity and quality at the cortical portion during bone regeneration in gene-defect mice in which the expression of bone cells is controlled, for example.