The Rhox family of homeobox-containing genes maps to three gene dense clusters, alpha, beta, and gamma, on the mouse X chromosome. Rhox genes are expressed primarily in reproductive and extra-embryonic tissues and may be regulated by colinear mechanisms. Uniquely among family members, Rhox4 is also expressed in the developing and adult thymus, where its striking restriction to the third pharyngeal pouch has suggested a role in lineage specification. In this article we describe a previously unreported duplication within the Rhox alpha locus that contains seven copies of Rhox4 and eight copies of Rhox2 and Rhox3 in a tandem array. We further show that all seven Rhox4 copies are expressed, although preferential expression occurs and differs between tissues. In contrast to reproductive tissues, we found no evidence of colinear expression of the Rhox alpha cluster during thymus development. All subspecies of mice examined contained multiple copies of Rhox4. However, the only predicted ortholog of Rhox4, rat Rhox4, is present in a single copy, suggesting that the duplications arose at the time of rat and mouse lineage divergence. Finally, no changes in Rhox4 expression were detected in mice with defects in thymus organogenesis, placing it upstream or outside of established transcriptional pathways.