We set out to determine whether near infrared reflectance spectroscopy (NIRS) combined with principal component analysis-linear discriminant analysis (LDA) or, variable selection techniques employing successive projection algorithm or genetic algorithm (GA) could evaluate the bone repair in cranial critical-size (5 mm) defect after stimulation with collagen sponge scaffold and/or infrared low-level laser therapy directly on the local. Forty-five Winstar rats were divided into nine groups of five each, namely: group H - healthy, n = 5 (without treatment and without cranial critical-size defect), (GI positive control - n = 5, 21 days or n = 5, 30 days) without treatment and with cranial critical-size defect; (GII-n = 5, 21 days or n = 5, 30 days) cranial critical-size defect filled with collagen sponge scaffold; (GIII-n = 5, 21 days or n = 5, 30 days) cranial critical-size defect submitted to low-level laser therapy; (GIV-n = 5, 21 days or n = 5, 30 days) cranial critical-size defect submitted to combined collagen sponge scaffold + low-level laser therapy treatment. In relation to the histological analysis, the collagen sponge scaffold + low-level laser therapy treatment group (GIV) 30 days showed the best result with the presence of secondary bone, immature bone (osteoid) and newly formed connective tissue (periosteum). GA-LDA model also successfully classified control class of the others classes. Thus, the results provided by the good-quality classification model revealed the feasibility of NIRS for application to evaluation of the wound healing in rat cranial defect, thanks to the short analysis time of a few seconds and nondestructive advantages of NIRS as an alternative approach for bone repair purposes. (C) 2017 American Institute of Chemical Engineers