Arteriovenous malformations (AVM) of the brain, errors in the development of the vasculature, produce high flow arteriovenous shunts. They steal blood from surrounding brain tissue, which is chronically hypoperfused. Hypoperfusion is a condition of inadequate tissue perfusion and oxygenation resulting in abnormal tissue metabolism. In the present study Fourier transform infrared (FTIR) spectroscopy was used to investigate the effects of hypoperfusion on rat cranial bone mineral and organic matrix at the molecular level. FTIR spectroscopic analysis revealed that in cranial bones of an experimental group the relative amount of carbonate and phosphate groups increased whereas that of protein (amide I) decreased. Curve-fitting analysis of the v(2) carbonate band showed that amounts of type A and type B carbonates increased slightly (p=0.423 for both) whereas, type L carbonate decreased slightly (p=0.522) in hypoperfused cranial bones. Analysis of the C-H region revealed a significant increase (p=0.037) in the lipid to protein ratio. Because the lipid content is high, hypoperfused cranial bone tissue is more prone to lipid peroxidation. Dialdehydes derived from lipid peroxidation can make cross-links with collagen and might lead to disturbances in the collagen cross-link profile. The 1660 cm(-1)/1690 cm(-1) partial area ratio derived from curve-fitting analysis of the Amide I band is sensitive to the relative amount of collagen non-reducible cross-link hydroxylysyl/lysylpyridinolines (Pyr) and reducible cross-link dihydroxylysinonorleucine (DHLNL) and this ratio reflects collagen maturity. In chronic hypoperfusion a significant decrease (p=0.004) was observed in this ratio. This means there were less mature collagen cross-links. Disturbances in the collagen maturation can affect mineralization process and lead to formation of pathologic structures in cranial bones. These findings clearly demonstrate that FTIR spectroscopy can be used to extract valuable information at molecular level, leading to better understanding of the effect of hypoperfusion on rat cranial bones.