Human pluripotent stem cells provide unique possibilities for in vitro studies of human cells in basic research, disease modeling as well as in industrial applications. By introducing relevant genome engineering technology, and thereby creating, for example, reporter cell lines, one will facilitate and improve safety pharmacology, toxicity testing, and can help the scientists to better understand pathological processes in humans. This review discusses how the merger of these two fields, human pluripotent stem cells and genome engineering, form extremely powerful tools and how they have been implemented already within the scientific community. In sharp contrast to immortalized human cell lines, which are both easy to expand and very simple to transfect, the genetically modified pluripotent stem cell line can be directed to a specific cell lineage and provide the user with highly relevant information. We highlight some of the challenges the field had to solve and how new technology advancements has removed the early bottlenecks.