Pluripotential embryonic stem cells (ESC) possess a unique property of being able to carry out nuclear reprogramming of somatic nuclei, as shown after cell fusion. The nuclear reprogramming activity has been applied for producing pluripotential stem cells from personal somatic cells through several new technologies, including cytoplasmic cell fusion and ES cell factor introduction. Targeted elimination of ESC-derived chromosome(s) following cell fusion-mediated reprogramming of somatic chromosomes is one of the new technologies for producing personalized stem cells. A universal chromosome elimination cassette (CEC) has been developed that confers drug resistance and GFP (green fluorescent protein) fluorescence, flanked by oppositely orientated loxP sites, to induce sister chromatid recombination and targeted chromosome loss. GFP-positive ESC generated with a CEC-integrated chromosome were hybridized with adult thymocytes and then exposed to Cre recombinase. This led to loss of GFP expression and elimination of the CEC-tagged chromosome. Targeted elimination of a pair of ESC-derived chromosome 6s, which are key chromosomes for maintaining pluripotency, demonstrated that the reprogrammed somatic factors are sufficient for the continued pluripotentiality of hybrid cells. Targeted chromosome elimination technology therefore offers a means for developing major histocompatibility complex-personalized or completely personalized pluripotential stem cell populations for use in a range of therapeutic applications.