The purpose of this study was to conduct a histomorphometric analysis of bone marrow-derived and adipose tissue-derived stem cells, associated with a xenograft block, in vertical bone constructions in rabbit calvaria. Ten rabbits received two xenograft blocks on the calvaria, after decortication of the parietal bone. The blocks were fixed with titanium screws. The blocks were combined with the bone marrow-derived mesenchymal stem cells in the bone marrow stem cell (BMSC) group (right side of the calvaria) or with the adipose tissue-derived mesenchymal stem cells in the adipose tissue stem cell (ATSC) group (left side of the calvaria). After 8 weeks, the animals were sacrificed and their parietal bones were fixed in 10% formalin for the histomorphometric analysis. The following parameters were evaluated—newly formed bone (NFB), xenogeneic residual particles (XRP), and non-mineralized tissue (NMT). The histomorphometric analysis revealed 11.9 ± 7.5% and 7.6 ± 5.6% for NFB, 22.14 ± 8.5% and 21.6 ± 8.5% for XRP, and 65.8 ± 10.4% and 70.8 ± 7.4% for NMT in groups BMSC and ATSC, respectively, with statistically significant differences in the NFB and the NMT between the groups, but no differences in the XRP. Therefore, it can be concluded that the bone marrow-derived stem cells seem to have more potential for the bone formation than do the adipose tissue-derived stem cells when used in combination with the xenogenous blocks in the vertical bone construction.