With uncertainty and the possibility of serious risks, stem cell based therapies should be introduced to clinical practice only after clinical trials demonstrate their efficacy and safety. The ethical issues related to current stem cell based therapies are examined based upon ethical principles. For the ethical conduct of clinical trials using stem cells, the guidelines for all clinical research should be followed. Because of highly innovative nature of such trials, special attention must be paid to rigorous scientific and ethics review in comparison of currently available treatments, assurance of voluntary informed consent and publication of findings of the clinical trial including negative results and adverse effects. International guidelines and Korean regulations are surveyed for justifiable medical use of unproven stem cell-based interventions. Key features include application of such innovative intervention only to a very small number of seriously ill patients, following a written protocol, approval from an ethics committee, informed consent, safety monitoring, follow-up data collection to evaluate effectiveness and adverse effects and transition to a formal clinical trial in a timely fashion after experiencing a few patients.