To investigate the effect of a factor-associated suicide (FAS) gene polymorphism on the death of chicken embryos, we genotyped 190 dead embryos and 69 normally developing embryos from 7200 hatching Short-Leg Yellow Chicken eggs, as well as 119 dead embryos and 69 normally developing embryos from 4650 hatching Yellow B Chicken eggs. The results showed that there were significant (P < 0.05) genotypic differences between dead and normally developing embryos for this FAS gene polymorphism, a SNP in exon 3 (NC_006093.2:g.6514A>C, rs15793179). Logistic regression revealed that Short-Leg Yellow Chicken embryos with genotype g.6514CC had a significantly (P < 0.01) higher risk of death than those with genotype g.6514AC. This polymorphism has the potential to be an effective tool when used in conjunction with traditional selection methods.