The formation of the body plan of bilaterians involves the determination of cell identity fields that ultimately result in the formation of specific anatomical structures. Hox genes have long been suggested to play a critical role in this process, encoding transcription factors strongly active during development that condition cellular differentiation. Their function seems to be tightly associated with their unique mode of transcription, where the order of a given Hox gene, within a cluster of related genes, defines the time and place of expression during development, a phenomenon known as colinearity. There are punctual exceptions to this transcriptional behaviour, adding complexity to the understanding of Hox gene’s regulation and function. Nevertheless, the precise expression domains that these genes assume suggest that refined regulatory mechanisms, which change over time and place, take action to instigate a particular expression profile. The discovery of the principles that govern Hox regulation has been a challenge, which recently has gained new impetus with the increasing knowledge of the genome, its products, and its epigenome. A fundamental part of this research has been the identification of the “players” acting upon Hox regulation. This effort led to the discovery of genomic regions that act as promoters, enhancers or insulators of Hox gene’s transcription. Additionally, micro- and long-non-coding RNAs, which contribute to the transcriptional or post-transcriptional control in specific cases, have been uncovered and the state-of-the-art is now heading towards understanding the impact of chromatin configuration and other epigenetic phenomena associated with the regulation of Hox gene expression and function. Here we review the current information available on the elements and mechanisms found so far to act on Hox gene regulation and discuss their hypothetical role in the evolution of the Hox-mediated developmental processes.