The severe sole effects of seizures on the cortical part of bone were reported in our previous study. However, the side effects of anti-epileptic drug therapy on bones has not been differentiated from the effects of the convulsive seizures, yet. This study provides the first report on differentiation of the effects of seizures and carbamazepine (a widely used antiepileptic drug) therapy on bones; 50mg/kg/day drug was given to genetically induced absence epileptic rats for five weeks. Distinct bone regions including cortical, trabecular, and growth plate in each of tibia, femur, and spine tissues were studied using Fourier transform infrared (FT-IR) imaging and Vickers microhardness test. Blood levels of vitamin D and bone turnover biomarkers were also measured. According to the FT-IR imaging results, both seizure and carbamazepine-treated groups, more dominantly the drug-treated group, had lower mineral content with altered collagen crosslinks and higher crystallinity, implying reduced bone strength. Lower microhardness values also supported lower mechanical strength in bones. The most affected bone tissue and region from seizures and treatment was found as the spine and cortical, respectively. While there was a reduction in vitamin D and calcium levels in both seizure and carbamazepin-treated groups, significantly elevated PTH and bone turnover biomarkers were only seen in the drug-treated group.