Bone morphogenetic protein 4 (BMP4) plays a crucial role in growth and development of mammals, especially for bone growth. The aim of the present study was to assess the association of polymorphism in BMP4 gene with growth traits in three goat breeds. In this study, on the basis of PCR-SSCP and DNA sequencing methods, two new silent mutation sites of A1986G and G2203A were identified in the intron 2, and one novel microsatellite of dinucleotide-repeated (CA) sequence was in the 3' flanking region. Associations between growth traits and BMP4 gene polymorphism were investigated, and significant statistical association results were found in body height, chest circumference and trunk index (P < 0.05). The result strongly suggested that the microsatellite located in BMP4 gene might be in linkage with the two new SNPs. Further investigations are required for detecting the polymorphism of this gene in a broad variety of goat breeds and populations.