Knowing that human embryonic stem cells (HESC) can be derived into several different cells types render these cells very attractive to cure diseases. Unless these stem cells are originated from the patient itself, they will be isolated from a donor, who is genetically unrelated to the recipient. This situation will mimic an allogenic transplantation with an immune response against the transplanted cells. The immunogenicity of the HESC and the potential of NK and T-cells to target HESC and the lineage derived from HESC have to be addressed. Several different tests do exist to analyse NK cells and T-cells activity against HESC and its progenitor cells. In this chapter review the capacity of NK and T cells against neural progenitor derived from HESC, through a classical and a novel approach that combined the phenotype and also the functionality of the effector cells. In addition, we also demonstrate in the same test that we can determine the lysis of the progenitor cells by flow cytometry.