Cortical and trabecular bone are both produced and maintained by the same cell types. At the microscopic scale they have a similar lamellar structure but at a macroscopic scale they are very different. Raman microscopy has been used to investigate compositional differences in the two bone types using bone from standard laboratory mice in physiological conditions. Clear differences were observed when complete spectra were compared by principal component analysis (PCA). Analysis of individual bands showed cortical bone to have compositional characteristics of older bone when compared with trabecular material, possibly due to the higher bone turnover traditionally reported in the trabecular compartment.