The purpose of this study was to evaluate the effect of etidronate (EHDP) on three-dimensional (3D) trabecular structure in ovariectomized (OVX) and sciatic neurectomized (NX) rats. Eight-week-old female Lewis rats received ovariectomy (n = 19) or sham operation (OVX-sham; n = 10). OVX rats received either vehicle (OVX-control; n = 9) or EHDP (OVX-EHDP; n = 10). Eight-week-old female Lewis rats received NX (n = 20) or sham operation (NX-sham; n = 10). NX rats received either vehicle (NX-control; n = 10) or EHDP (NX-EHDP; n = 10). EHDP at 5 mg/kg or vehicle was subcutaneously injected 5 days a week. The treatment was initiated 2 weeks after surgery and was continued for 2 weeks. At 12 weeks of age, the rats were killed, and we scanned the proximal metaphysis of the tibia; this was done using micro-CT; (μ CT20; SCANCO Medical). The recovery of structural parameters was not complete in NX rats compared to OVX rats. The 3D micro-CT images showed that the subcortical spongiosa, which was preserved in OVX rats, had marked loss in NX rats. Furthermore, these trabeculae were not restored after the EHDP treatment. In conclusion, the mechanical driving of the control of trabecular structure is inactive in NX, and EHDP treatment for 2 weeks does not restore this condition.