Lipoprotein Lipase (LPL), a key enzyme in lipid metabolism, catalyses the hydrolysis of triglycerides (TG) from TG-rich lipoproteins, and serves a bridging function that enhances the cellular uptake of lipoproteins. By sequencing, we identified a four novel SNPs; one SNP involved a Gly→Arg AA substitution at position 23 of the signal peptide, and three SNPs in the intron I (KP261023) of the LPL locus. A protocol for rapid efficient simultaneous genotyping of LPL variants using the primer extension method (PEA) was described, and a total of 230 animals belonging to two goat breeds: White Shorthaired goat (n=177), and Brown Shorthaired goat (n=103) were genotyped. A total 15 genotype combinations were detected in tested goat populations.