Recent research has demonstrated that not only haemodynamic factors but also genetic programmes control arterial-venous cell fate and blood vessel identity. The identification of arteries and veins was previously based solely on morphological criteria and is now greatly facilitated by specific molecular markers. Moreover, signalling pathways controlling the arterial-venous decision during embryonic development have been outlined for the first time. This review gives an up-to-date overview of differentially expressed genes and the regulatory processes leading to the differentiation of arteries and veins.