Chromosomal abnormalities are common in human embryos and cause implantation failure, early pregnancy losses, and birth defects in practice of assisted reproductive technology (ART). Non-invasive chromosome screening (NICS) is an emerging technology that enables the selection of chromosomal-balanced embryos, without performing invasive embryo biopsy. Here we report the full protocol of NICS, which includes culture medium pretreatment, whole genome amplification (WGA) by multiple annealing and looping-based amplification cycles (MALBAC), library preparation for next generation sequencing (NGS) and NGS data analysis. To validate the reliability and efficiency of NICS, we have already performed NICS on 27 transfer cycles in 23 couples with balanced translocation, azoospermia, recurrent pregnancy loss (RPL), or recurrent implantation failure (RIF), 17 of them have achieved successful clinical pregnancies, and 9 among them have already obtained healthy live births. No pregnancy loss has been reported thus far. The NICS method avoids the need for embryo biopsy and therefore substantially increases the safety of its use.