Previous reports have shown that epithelial-to-mesenchymal transition (EMT) indicates the importance of transforming growth factor-β (TGF-β) signalling in the pathogenesis of systemic sclerosis (SSc). However, the underlying molecular mechanisms of EMT are not fully understood. Brachyury, an evolutionarily conserved transcription factor, was recently identified as an important factor that promotes EMT in human carcinoma cell lines. However, there is no evidence indicating that brachyury is involved in EMT in SSc. The expression of brachyury and collagen was investigated in cultures of dermal fibroblasts and skin sections derived from SSc patients and healthy controls. Brachyury and collagen expression were determined by immunohistochemistry and immunoblotting, respectively, and mRNA for both was analysed using real-time PCR. Brachyury was overexpressed in SSc dermal fibroblasts both in vivo and in vitro, and this overexpression was inhibited by TGF-β1 inhibitor. Brachyury siRNA reduced mRNA and protein expression levels of type I collagen in normal and SSc dermal fibroblasts, but did not decrease the levels of major disease-related cytokines. Furthermore, brachyury levels were significantly increased in skin samples of SSc patients relative to healthy controls. The up-regulation of brachyury in response to activated endogenous TGF-β signalling may play a role in constitutive up-regulation of collagen in SSc fibroblasts. Further studies assessing the regulatory mechanism of tissue fibrosis induced by brachyury in SSc skin may lead to a better understanding of the pathogenesis, new diagnostic methods, and new therapeutic approaches using siRNAs.