Tissue engineering of bone, by combining multipotent stromal cells (MSCs) with osteoconductive scaffolds, has not yet yielded any clinically useful applications so far. The fate and contribution of the seeded cells are not sufficiently clarified, especially at clinically relevant locations. Therefore, we investigated cell proliferation around the spine and at ectopic sites using noninvasive in vivo bioluminescence imaging (BLI) in relation to new bone formation. Goat MSCs were lentivirally transduced to express luciferase. After showing both correlation between MSC viability and BLI signal as well as survival and osteogenic capacity of these cells ectopically in mice, they were seeded on ceramic scaffolds and implanted in immunodeficient rats at two levels in the spine for spinal fusion as well as subcutaneously. Nontransduced MSCs were used as a control group. All rats were monitored at day 1 and after that weekly until termination at week 7. In mice a BLI signal was observed during the whole observation period, indicating survival of the seeded MSCs, which was accompanied by osteogenic differentiation in vivo. However, these same MSCs showed a different response in the rat model, where the BLI signal was present until day 14, both in the spine and ectopically, indicating that MSCs were able to survive at least 2 weeks of implantation. Only when the signal was still present after the total implantation period ectopically, which only occurred in one rat, new bone was formed extensively and the implanted MSCs were responsible for this bone formation. Ectopically, neither a reduced proliferative group (irradiated) nor a group in which the cells were devitalized by liquid nitrogen and the produced extracellular matrix remained (matrix group) resulted in bone formation. This suggests that the release of soluble factors or the presence of an extracellular matrix is not enough to induce bone formation. For the spinal location, the question remains whether the implanted MSCs contribute to the bone regeneration or that the principal mechanism of MSC activity is through the release of soluble mediators.