This study was designed to investigate an effective method for the derivation of human embryonic stem cells (hESC) from poor quality embryos discarded from in vitro fertilization (IVF) laboratories. Poor quality embryos were donated from IVF center on day 3 and cultured in a blastocyst medium for 2 days, and then in a blastocyst optimum culture medium for additional 2 days. The isolated inner cell masses (ICM) were inoculated onto the feeder layer of mouse embryonic fibroblasts for subcultivation. The biological characterizations and differentiation capability of these cells were examined after at least 15 passages. Forty-two embryos developed to expanded blastocysts or hatched blastocysts and ICMs were successfully isolated from all embryos. Six new hESC lines were established after further culture. All hESC lines were positive for stage-specific embryonic antigen SSEA-4, TRA-1-81, TRA-1-60 markers and negative for SSEA-1 marker. They showed a high level of alkaline phosphatase activity, positive expression of transcription factor Oct-4. Furthermore, these cells had the potential to form both embryoid bodies in vitro and teratomas in vivo. Five hESC lines had normal karyotypes and one had trisomy 13. In this paper we described a stable and effective system for hESC isolation and established six new hESC lines, which will provide an excellent experimental model for cell therapy, developmental biology and genetic research.