Bone defects are a challenging clinical situation, and the development of hydroxyapatite-based biomaterials is a prolific research field that, in addition, can be joined by stem cells and growth factors in order to deal with the problem. This study compares the use of synthetic hydroxyapatite and xenograft, used pure or enriched with bone marrow mononuclear fraction for the regeneration of critical size bone defects in rat calvaria through histomorphometric (Masson’s staining) and immunohistochemical (anti-VEGF, anti-osteopontin) analysis. Forty young adult male rats were divided into five groups (n = 8). Animals were submitted to critical size bone defects (Ø = 8 mm) in the temporoparietal region. In the control group, there was no biomaterial placement in the critical bone defects; in group 1, it was filled with synthetic hydroxyapatite; in group 2, it was filled with xenograft; in group 3, it was filled with synthetic hydroxyapatite, enriched with bone marrow mononuclear fraction (BMMF), and in group 4 it was filled with xenograft, enriched with BMMF. After eight weeks, all groups were euthanized, and histological section images were captured and analyzed. Data analysis showed that in groups 1, 2, 3 and 4 (received biomaterials and biomaterials plus BMMF), a significant enhancement in new bone matrix formation was observed in relation to the control group. However, BMMF-enriched groups did not differ from hydroxyapatite-based biomaterials-only groups. Therefore, in this experimental model, BMMF did not enhance hydroxyapatite-based biomaterials’ potential to induce bone matrix and related mediators.