The complexities of modern science are not adequately reflected in many bioethical discussions. This is especially problematic in highly contested cases where there is significant pressure to generate clinical applications fast, as in stem cell research. In those cases a more integrated approach to bioethics, which we call systems bioethics, can provide a useful framework to address ethical and policy issues. Much as systems biology brings together different experimental and methodological approaches in an integrative way, systems bioethics integrates aspects of the history and philosophy of science, social and political theory, and normative analysis with the science in question. In this paper we outline how a careful analysis of the science of stem cell research can help to refocus the discussions related to the clinical applications of stem cells. We show how inaccurate or inadequate scientific assumptions help to create a set of unrealistic expectations and badly inform ethical deliberations and policy development. Systems bioethics offers resources for moving beyond the current impasse.