Microsurgical manipulations were performed in ovo to identify the tissues that are required for conferring inner ear patterning. Our results show that the hindbrain, namely rhombomeres 5 and 6, are required for the formation and patterning of the cochlear duct (basilar papilla). Rhombomere 5 and its underlying notochord appear to be important for the growth of the cochlear duct, whereas rhomobomere 6 and its respective notochord are required for cochlear patterning. Rotating the segment of hindbrain from rhombomere 5 to rhombomere 6 along the anteroposterior axis affects cochlear duct formation but has no effect on the development of vestibular structures. The signaling molecules intrinsic to these tissues are distinct from Sonic Hedgehog, which has been shown to be required for cochlear duct outgrowth. In contrast, otic mesenchyme adjacent to the developing inner ear provides anteroposterior axial information to pattern the anterior and posterior canals and ampullae.