This study aims to identify DNA marker related to health index which is derived from fatty acid composition of Hanwoo meat. We investigated a genetic association between two SNPs (-867G>C and 878C>T) of SCD gene and health indexes. Two health index values (index of atherogenicity and index of thrombogenicity) were derived from a combination of fatty acid composition. Phenotypic correlation indicated that oleic acid (C18:1) was negatively correlated to index of atherogenicity (-0.84) and index of thrombogenicity (-0.91), respectively. Statistical analysis revealed that 878T>C SNP was significantly associated with IA (index of atherogenicity, p=0.012) and IT (index of thrombogenicity, p=0.006). There was no association between the regulatory SNPs (-867G>C and -877Gdel) and health indexes. Haplotype analysis detected 4 main haplotype (GdelT; 0.004, GdelC; 0.344, CGT; 0.350 and CGC; 0.261) in Hanwoo. The GdelT haplotype was significant on IA and IT. The effect of GdelT haplotype showed increasing IA and IT values, while GdelC haplotype has a decreasing IA and IT value in Hanwoo. In conclusion, the 878C>T SNP in the SCD gene seems to have an effect on this health index and might be implemented into animal breeding program.