Objective: The aim of this research is to evaluate the value of the histological score based on a histological record compared to the histometry for monitoring cranial bone defect healing. Methods: We designed a case -control study with a control and a study group. For a number of 60 CD1 mice representing the study group, a bone defect in the cranial bone was surgically induced and grafted with bone grafts obtained by tissue engineering. Bone grafts were obtained using embryonic stem cells seeded on a scaffold obtained from the red deer antler, and osteogenic basal and complex medium was used as differentiation medium. For other 30 CD1 mice representing the control group, a bone defect in the cranial bone was induced and left to heal without grafts. The regeneration process was assessed after 2 and 4 months using the histological healing scoring system and histometry. Results: The healing score was statistically significantly correlated with the defect size obtained by means of histometry (p<0.001). The evaluation of the parameters comprised in the healing score shows that regeneration of the bone diastasis was the most advanced in the group sacrificed at 4 months after plasty, which employed embryonic stem cells, a complex osteogenic differentiation medium and deer antler as scaffold. Conclusion: histological method based on a histological score is a valuable quantification system of bone regeneration comparable to histometry. Clinical Relevance: This study proves that the presented histological score can help the clinician in the process of bone regeneration evaluation.