Objective To explore the effect of chromosomal polymorphic variations on the outcome of in vitro fertilization/intracytoplasmic sperm injection-embryo transfer (IVF/ICSI-ET) treatment for infertile couples. Methods In this retrospective study, 1 108 infertile couples, who received their first IVF/ICSI-ET treatment cycles in Reproductive Medicine Center of Changhai Hospital of Second Military Medical University from Mar. 2015 to Jun. 2016, were included and divided into two groups:normal chromosomal group (the infertile couples with normal chromosome) and chromosomal polymorphic group (with chromosomal polymorphic variations). The embryo implantation rate, clinical pregnancy rate (CPR), early abortion rate and live birth rate (LBR) after IVF/ICSI-ET treatment were compared and analyzed. Results A total of 1 108 infertile couples received IVF/ICSI-ET treatment were enrolled, with 69 in the chromosomal polymorphic group, and 1 039 in the normal chromosomal group. There were no significant differences between the two groups in embryo implantation rate (34.91% vs 34.62%, P>0.05), CPR (49.09% vs 50.72%, P>0.05), early abortion rate (11.37% vs 8.57%, P>0.05) or LBR (41.67% vs 43.47%, P>0.05). Conclusion Chromosomal polymorphisms appear to have no effect on the outcome of IVF/ICSI-ET treatment for infertile couples.