Mox1 and Mox2 homeobox genes have been shown to be critical in axial skeleton and in limb muscle development respectively. Pax1 and Pax3 gene products are also implicated in these processes. Mox and Pax expression patterns are highly overlapping both spatially and temporally during embryonic development. We show here for the first time that Mox proteins physically interact with Pax1 and Pax3 using the yeast two-hybrid protein interaction assay as well as in vitro biochemical assays. There is a strong preference of Mox1 to associate with Pax1 rather than Pax3 and of Mox2 to associate with Pax3 rather than Pax1. The observed interactions are mediated through the homeodomain of Mox.