Applications of imaging techniques to visualize stem cells for monitoring, control and treatment of biological systems, in particular the brain, is at the forefront of investigations. These approaches involve the identification of stem and precursor cells that may be of various origins, but are related to specific clinical conditions, and the choice of the appropriate markers to achieve the required imaging while minimizing the side effects. This article will review examples of the contrast agent design for rational approaches in stem cell imaging. Potential pitfalls or side effects associated with contrast agents, in particular iron oxide nanoparticles, for cell labelling are also discussed.