Homeobox genes encode important developmental control proteins. In vertebrates, those encoding the proteins of the HOX class and their most closely related families, including paraHOX and metaHOX classes, are clustered in paralogous regions (or paralogons). We show that the majority of the other homeobox genes (we called contraHOX) can also be clustered and belong to paralogons in humans. This suggests that they duplicated during vertebrate evolution along the same processes as the HOX genes. We tentatively assembled several paralogons in superparalogons. One of the superparalogons contains the contraHOX genes. These observations were extended to hundreds of genes, and allowed to describe a primary human genome paralogy map.