Purpose To assess the genetic and epigenetic status of parthenogenetic human embryonic stem cells (phESCs). Methods Cytogenetics, X chromosome inactivation (XCI) and gene expression patterns were analyzed in one phESC line (FY-phES-018) that was derived from our laboratory. Results FY-phES-018 cells displayed the classical characteristics of normal hESCs. These cells had a 46, XX karyotype, and no inactive X chromosomes were observed before passage 20. After being cultured long term in vitro, some cells lost one X, and the proportion of cells with only one X gradually increased. At passage 35, almost all the cells displayed a 45, XO karyotype. Interestingly, at passage 45, the recovery of the X-chromosome was observed, and XCI became detectable; the mosaic ratio of 46, XX to 45, XO was 67:33. After passage 60, most cells displayed the 46, XX karyotype again with a mosaic ratio of 97:3. Some aberrant genomic imprinting was also observed in these cells. Conclusions The phESCs line FY-phES-018 is both genetically and epigenetically unstable; therefore, further research is needed before using these cells.