Cleft lip and cleft palate are among the most common congenital birth defects affecting the craniofacial region. Development of the head and face requires tight molecular control of time- and site-specific events. The importance of these regulatory processes is seen when even a small error in the molecular hierarchy has devastating effects on normal development leading to clefting phenotypes. Recently, a number of isolated cleft palate cases have been identified as a result of mutations in SATB2. This thesis reveals that SATB2 expression is conserved across vertebrate lineages. SATB2 is expressed throughout secondary palate development and most abundant in the anterior region of the developing mouse palatal shelves. On fusion of the palatal shelves, Satb2 expression is observed in the ossification centres of the palate. Newborn Satb2-/- mice exhibit cleft palate, fewer disorganised palatal rugae, expansion of the soft palate and hypoplasia of the bones forming the hard palate.Correlating with Satb2 expression during palatal shelf growth, Satb2-/- embryos exhibit altered morphology of the anterior palatal shelves as a result of aberrant cell proliferation. Moreover, the anterior region of the palate lost the potential to fuse, which is underlined by the regional absence of Tgfb3 in the medial edge epithelia. Temporo-spatial expression analysis of the palatal shelves of Satb2-/- embryos revealed marked reduction of Shh in the palatal rugae and significant up-regulation of Fgf10 in the anterior palate mesenchyme, which correlates with the abnormal palatal rugae. Moreover, genes implicated in Bmp signalling including Bmp4, Msx1 and Pax9, which control anterior palate growth, were up-regulated correlating with increased proliferation in the anterior Satb2-/- palatal shelf mesenchyme. Microarray analysis of E13.5 Satb2-/- palatal shelves revealed down-regulation of a group of genes promoting bone development and up-regulation of inhibitors of bone development, which correlates with hypoplasia of the hard palate. Moreover, microarray analysis revealed down-regulation of En1, Cadm3, Sema3e and Shox2, which are specific for the anterior region of the palatal shelves, in Satb2-/- embryos. Interestingly, Tbx22, which is expressed specifically in the posterior region of palatal shelves, was up-regulated resulting in ectopic extension into the anterior region of Satb2-/- palatal shelves. As a result, the well-defined Shox2 and Tbx22 expression border was disrupted, suggesting that the anterior palate mesenchyme had lost its molecular identity. Bioinformatics analysis revealed Satb2-binding motifs around Shox2 and Tbx22, suggesting direct regulation. In addition, Shox2 and Tbx22 are under indirect Bmp signalling. As the region upstream from the Satb2 promoter contains Smad-binding sites, it can be hypothesised that Satb2 receives Bmp signals in order to regulate Shox2 and Tbx22. Motif analysis also revealed potential Satb2-binding sites around Bmp4, Msx1 and Pax9, suggesting that Satb2 may be involved in a feedback loop, thereby fine-tuning the Bmp signalling during secondary palate development.