In the perspective of clinical translation of stem cell research, it would be advantageous to develop new techniques to detect donor cells after transplantation to track their fate and thus better understand their role in regeneration of damaged and diseased tissues. In this study we use X-ray computed microtomography for three-dimensional visualization of stem cells that were labeled with magnetic nanoparticles and transplanted via intra-arterial infusion. We show that X-ray computed microtomography offers the possibility to detect with high definition and resolution human cells after transplantation, and opens new possibilities for both experimental stem cell research.