Abstract: Genetic variations of MDFI gene were detected by PCR-SSCP and DNA sequencing in 116 Haimen goats at 1.5 years old. Association analyses were conducted to evaluate the effect of genotypes of polymorphic loci on body size traits of the breed. The results showed that two SNPs of Haimen goats in MDFI gene were found in extron 3 and extron 4, and caused one nonsense mutation and one missense mutation. The genotypes of P4 and P5 loci had significant associations with the body height, circumference of cannon bone and chest circumference of Haimen goat（P<0.05）. The associations were appropriate for the auxiliary mark of molecular breeding.