The study of human development and diseases relies on analysis of samples obtained and manipulated ex-vivo. It is critical in such studies to know the provenance and confirm that the identity of these materials is correct. Furthermore, it is critical to confirm that once manipulated, these cells have the desired differentiated characteristics and have maintained genome integrity. In this study, we describe a complete workflow for quality control of ex-vivo manipulated human cells, including cell lines, induced pluripotent stem cells (iPSC) and chimeric receptor T-cells (CAR-T). Analysis of short tandem repeats (STRs) was used as a molecular “fingerprint” to track and confirm the identity of the manipulated cells. Pluripotency of iPCS was determined by analyzing the expression of a panel of differentiation-state specific genes. Genomic integrity was analyzed by molecular karyotyping using high-resolution microarrays. The presence or absence of pathogenic oncogenes in the manipulated cells was determined by sequencing a panel of oncogenic hotspot loci. Together, these results and robust workflows provides a comprehensive quality control of human cells, critical for the establishing clinical research-compliant ex-vivo manipulation methods.