This study aimed to assess bone repair in defects grafted or not with hydroxyapatite (HA) on healthy and iron-deficiency anemia (IDA) rats submitted or not to LED phototherapy (LED-PT) by Raman spectroscopy. The animals were divided in eight groups with five rats each: Clot; Clot + LED; IDA + Clot; IDA + LED; Graft; Graft + LED; IDA + Graft; and IDA + Graft + LED. When appropriated, irradiation with IR LED (λ850 ± 10 nm, 150 mW, CW, Φ = 0.5 cm(2), 16 J/cm(2), 15 days) was carried out. Raman shifts: ∼ 960 [symmetric PO4 stretching (phosphate apatite)], ∼ 1,070 [symmetric CO3 stretching (B-type carbonate apatite)], and ∼ 1,454 cm(-1) [CH2/CH3 bending in organics (protein)] were analyzed. The mean peak values for ∼ 960, ∼ 1,070, and ∼ 1,454 cm(-1) were nonsignificantly different on healthy or anemic rats. The group IDA + Graft + LED showed the lowest mean values for the peak ∼ 960 cm(-1) when compared with the irradiated IDA group or not (p ≤ 0.001; p ≤ 0.001). The association of LED-PT and HA-graft showed lowest mean peak at ∼ 1,454 cm(-1) for the IDA rats. The results of this study indicated higher HA peaks as well as a decrease in the level of organic components on healthy animals when graft and LED phototherapy are associated. In the other hand, IDA condition interfered in the graft incorporation to the bone as LED phototherapy only improved bone repair when graft was not used.