Cell-based reconstruction therapies promise new therapeutic opportunities for bone regeneration. Unrestricted somatic stem cells (USSC) from cord blood and embryonic stem cells (ESCs) can be differentiated into osteogenic cells. The purpose of this in vivo study was to compare their ability to induce ectopic bone formation in vivo. Human USSCs and murine ESCs were cultured as both monolayer cultures and micromasses and seeded on insoluble collagenous bone matrix (ICBM). One week and 1, 2, and 3 months after implanting the constructs in immune-deficient rats, computed tomography scans were performed to detect any calcification. Subsequently, the implanted constructs were examined histologically. The radiological examination showed a steep increase in the mineralized bone-like tissue in the USSC groups. This increase can be considered as statistically significant compared to the basic value. Moreover, the volume and the calcium portion measured by computed tomography scans were about 10 times higher than in the ESC group. The volume of mineralization in the ESC group increased to a much smaller extent over the course of time, and the control group (ICBM without cells) showed almost no alterations during the study. The histological examinations parallel the radiological findings. Cord blood stem cells in combination with ICBM-induced ectopic bone formation in vivo are stronger than ESCs.