This work aimed the assessment of the biochemical changes during bone mineralization induced by laser and LED irradiation in an animal model of bone repair using a spectral model based on Raman spectroscopy. Six groups were studied: Clot, Laser (λ780 nm, 70 mW), LED (λ850 nm ± 10 nm, 150 mW), Biomaterial (biphasic synthetic microgranular hydroxyapatite (HA) + β-tricalcium phosphate), Laser + Biomaterial and LED + Biomaterial. When indicated, defects were further irradiated at 48 h interval during 2 wks, 20 J/cm2 per session. At 15th and 30th days, femurs were dissected and spectra of the defects were collected. Raman spectra were submitted to a model to estimate the relative amount of collagen, phosphate HA and carbonate HA, by using spectra of pure collagen, biomaterial and basal bone, respectively. At 15th days, the use of biomaterial associated to phototherapy reduced the collagen formation, whereas the amount of carbonate HA was not different in all groups. The phosphate HA was higher in the groups that received biomaterial grafts. At 30th days, it was observed an increase of collagen for the group Laser + Biomaterial, and a reduction in the carbonate HA for the LED + Biomaterial. The phosphate HA was higher for the groups LED + Biomaterial and Laser + Biomaterial, while decreased for the group Biomaterial. These results indicated that the use of Laser and LED phototherapies improved the repair of bone defects grafted with the biomaterial by increasing the collagen deposition and phosphate HA.