Recently, consumers have become increasingly health-conscious and demand not only palatable but also health-beneficial meat in the market. In Korea, degree of the intramuscular fat deposit (marbling) is one of the crucial indicators to judge beef quality. Thus, the fatty acids profile in beef is important because it affects both flavor and health-benefit. Various trials have been conducted to change fatty acids profile into health-beneficial composition, such as poly-unsaturated fatty acids-abundant meat, in Korean beef. The fatty acid binding protein 4 (FABP4) gene is a cytosolic protein abundantly expressed in adipocyte and plays an important role on lipid synthesis and intracellular fatty acid trafficking. An SNP located on the splice site variation between the third exon and the third intron of bovine FABP4 showed a statistically significant effect on intramuscular fatty acid deposition. The aim of this study was to investigate the relationship between SNP within the third intron region of FABP4 and fatty acids profile of longissimus dorsi area in Korean cattle. We sequenced the third intron region of bovine FABP4. Among this SNPs, the g.3996 C>T SNP show statistically significant effect on oleic acid and polyunsaturated fatty acids (P < 0.001). Especially, the animals with CC genotype have a lower ratio of omega-6/-3 fatty acid (5.4:1) than the ratio of animals with TT genotypes (9.9:1). Therefore, our result suggest that g.3996 C>T intronic SNP will be used as a useful marker-assisted selection for breeding on fatty acids profile of Korean cattle.