Bisphosphonates (BPs) are known to increase bone mineral density, but it is not known how this increase manifests at low hierarchic levels of the bone structure. The present study aimed to clarify the effects of the long-term use of clodronate on the microstructure and chemical composition of bone. The second lumbar vertebral body (L2) in growing rats, subjected to 32 weeks' treatment with clodronate at either a therapeutic dose of 2 mg/kg, or a high dose of 10 mg/kg, or physiological saline (control group), was studied by scanning electron microscopy for morphology, by backscattered electron image (BSE) for density, and by energy dispersive spectrometry for material analysis. BSE images showed that the degree of mineralization in the different areas of trabecular bone of the vertebral body varied in both the control and the study groups, but this variation seemed to be different in the control and study groups. BSE analysis showed that there was more high-density bone (white area) in the low-dose clodronate group than in the controls, but the difference between the high-dose clodronate group and the control group was not significant. The density of the white area (high-density bone) was slightly increased in the low-dose clodronate group. There were no differences in the density of the gray area (low-density bone) between the groups. Neither the distribution of Ca, P, or Mg, nor the total mineral content, was affected by the clodronate treatment. Our results indicate that long-term clodronate treatment at the therapeutic level increases the proportion of high-density bone in the vertebral body in non-osteoporotic rats.