In vertebrates, the paraxial mesoderm differentiates into several structures, including the axial skeleton. The genetic mechanisms that control positional information in the paraxial mesoderm along the anterior-posterior axis are responsible for the development of a skeleton with the appropriate vertebral formula, i.e. a specific number of cervical, thoracic, lumbar, sacral and caudal vertebrae. These control mechanisms are complex and involve molecules of different kinds, including transcription factors, like those encoded by the Hox genes, and signalling molecules, like those involved in Gdf11, FGF, retinoic acid or WNT signalling. Recent experiments indicate that most of the positional information for the paraxial mesoderm is encoded during the initial steps of its development in the presomitic mesoderm, although it is only decoded later during differentiation of the somites. The genesis of positional identity may be linked to the process of somitogenesis, which also occurs in the presomitic mesoderm as a result of complex interactions involving oscillatory activity of components of the Notch and WNT signalling pathways and antagonistic gradients of FGF/WNT and retinoic acid. The possible connections between Hox genes and all these signalling processes to generate a properly patterned axial skeleton are discussed in this review.