Human embryonic stem cells (hESCs) are capable of differentiation into every cell type of the human being. They are under extensive investigation for their regenerative potential in a variety of debilitating diseases. However, the field of hESC research is still in its infancy, as there are several critical issues that need to be resolved before clinical translation. Two major concerns are the ability of undifferentiated hESCs to form teratomas and the possibility of a provoked immune reaction after transplantation of hESCs into a new host. Therefore, it is imperative to develop noninvasive imaging modalities that allow for longitudinal, repetitive, and quantitative assessment of transplanted cell survival, proliferation, and migration in vivo. Reporter gene-based molecular imaging offers these characteristics and has great potential in the field of stem cell therapy. Moreover, it has recently been shown that reporter gene imaging can be combined with therapeutic strategies. Here, we provide an outline of the current status of hESC research and discuss the concerns of tumorigenicity and immunogenicity. Furthermore, we describe how molecular imaging can be utilized to follow and resolve these issues.