The associations between AGPAT6 gene polymorphisms and body size traits (body height, body length, chest circumference) were investigated in 549 Xinong Saanen and Guanzhong dairy goats using PCR-RFLP techniques. Four single nucleotide polymorphisms (SNPs) including 5'UTR (g.152G ＞ C), intron2 (g.8124G ＞ A), exon4 (g.9263C ＞ G) and 3’UTR (g.16436G ＞ A) were detected in four loci (P1, P2, P4 and P10) respectively. The population genetic analysis showed that P2, P4 and P10 possessed intermediate polymorphism. The association study revealed that none of the four SNPs detected had a significant effect on the body traits in the two goat breeds (P ＞ 0.05).