Abstract: In order to investigate the polymorphism of MSTN gene in the 5′UTR region and its effect on body size indexes（body height, body length and chest circumference） of Yangyuan donkeys, 70 yangyuan donkeys over 2 years old were measured. PCR-SSCP technique was used to detect the polymorphic loci in the 5′UTR region of MSTN gene, and the differences of body size traits among different genotypes were analyzed. The results showed that there was g.229 T＞C mutation in the 5′UTR region of MSTN gene of Yangyuan donkeys, which produced TT, CC and TC genotypes. There were no significant differences in body height and body length among different genotypes（P＞0.05）, but chest circumference of CC genotype was significantly larger than that of the other two genotypes（P＜0.05）. The results indicated that site 229 could be a candidate marker for selection and breeding of Yangyuan donkeys.