Hypercholesterolemia is associated with deterioration of bone tissue. Trough Raman spectroscopy, the present study aimed to assess the molecular changes in terms of mineral and organic bone-tissue remodeling in low-density lipoprotein receptor gene knockout mice (LDLr−/−) submitted to treadmill aerobic training. In order to evaluate alterations in trabecular bone and cartilage surface, neck and head femoral were assessed into four groups: (CON, n=7), the 1) animals did not perform any physical activity and had hypercholesterolemia (CON, n=7); The trained groups where animals underwent a protocols of low, moderate and high training for 8weeks and 4 times per week on a treadmill with progressive intensities: running speed (8–13m/min) and time of exercise (20-60min). These progressive intensities were needed to adjust the working load for the physical training to 2) 30–49% (LOW, n=7), 3) 50–79% (MOD, n=7), and 4) 80–100% (HIGH, n=7) of the maximum running speed. Each group was examined for molecular changes in both bone phases (mineral and organic) using principal components analysis (PCA). All exercised groups showed a significant increase (p<0.05) of bone remodeling in trabecular area and a higher content of proteins (organic content) in cartilage independently of physical activity intensity. Thus, this work demonstrated that physical training could act as a bone-protector factor in hyperlipidemic animal model as well as Raman technique associated with PCA analysis may be feasible methodology for assessment or monitoring of bone at the molecular level.