In amniote embryos, three kidneys – the pronephros (a transient embryonic structure), the mesonephros (the embryonic kidney) and the metanephros (the adult kidney) – form sequentially along the anterior-posterior (AP) axis of the intermediate mesoderm (IM). Here (p. 4143), Thomas Schultheiss and colleagues investigate AP patterning in the mesoderm by analysing the specification of the avian embryonic nephric duct – an unbranched epithelial tube that originates in the anterior IM. Using quail-chick chimaeric embryos, the researchers show that nephric duct specification occurs early in development when IM precursor cells are still in the primitive streak. HoxB4, they report, is expressed in nephric duct precursors from the primitive streak stage onwards, whereas the more posterior Hox gene HoxA6 is expressed in non-duct IM. Notably, misexpression of HoxA6 in the duct-forming regions of the IM represses duct formation. Together, these results indicate that Hox genes regulate AP patterning in the IM and provide new insights into general mesodermal patterning along the AP axis and into kidney evolution.