The aim of this study was to determine whether sciatic nerve injury (SNI) can cause trabecular bone loss in not only the tibia, but also the lumbar vertebrae, and to investigate the correlation between baseline bone quantity (BV/TV, bone volume fraction) and the magnitude and rate of bone loss. Sixteen male C57BL/6 mice were used. Sciatic neurectomy (SNx) was carried out on both hind limbs of eight mice. The tibiae (T) and fourth lumbar vertebrae (L4) were scanned by in-vivo micro-computed tomography (micro-CT) before and at 2 weeks and 4 weeks after SNx. At 2 weeks and 4 weeks, BV/TVs in T and L4 were significantly lower in the SNx group than the non-SNx group (p < 0.05). There were significant negative correlations between BV/TV at 0 weeks and the relative variations in L4 at 2 weeks or in T at 4 weeks (p < 0.05). These results indicate that SNI can cause significant bone loss in the lumbar vertebrae and tibiae. The magnitude and rate of bone loss following SNI is affected by baseline bone quantity.