In this chapter, we consider the question of how the ordered clusters of Hox genes arose during evolution. Since ordered Hox clusters are found in all major superphyla, we have to assume that the Hox clusters arose before the Cambrian "explosion" giving rise to all of these taxa. Based on his studies of the bithorax complex (BX-C) in Drosophila Lewis considered the ground state to be the mesothoracic segment (T2) since the deletion of all of the genes of the BX-C leads to a transformation of all segments from T3 to A8/9 (the last abdominal segment) into T2 segments. We define the developmental ground state genetically, by assuming that loss-of-function mutants lead to transformations toward the ground state, whereas gain-of-function mutants lead to homeotic transformations away from the ground state. By this definition, T2 also represents the developmental ground state, if one includes the anterior genes, that is, those of the Antennapedia complex. We have reconstructed the evolution of the Hox cluster on the basis of known genetic mechanisms which involve unequal crossover and lead from an urhox gene, first to an anterior and a posterior gene and subsequently to intermediate genes which are progressively inserted, between the anterior and posterior genes. These intermediate genes are recombinant due to unequal crossover, whereas the anterior and posterior genes are not affected and therefore had the longest time to diverge from the urhox gene. The molecular phylogenetic analysis strongly supports this model. We consider the ground state to be both developmental and evolutionary and to represent the prototypic body segment. It corresponds to T2 and is specified by Antennapedia or Hox6, respectively. Experiments in the mouse also suggest that the ground state is a thoracic segment. Evolution leads from the prototypic segment to segmental divergence in both the anterior and posterior direction. The most anterior head and tail segments are specified by homeobox genes localized outside of the cluster.