The ability to produce rhythmic motor behaviours linked to a respiratory function is a property of the brainstem reticular formation, which has been remarkably conserved during the evolution of vertebrate. The functional scaffold of brainstem neuronal circuits is first set in the embryonic neural tube, when the hindbrain is partitioned along the anterior-posterior axis into polyclonal developmental compartments called rhombomeres (r). In the hindbrain, the Hox genes provide cells with positional information and rhombomeric identity along the antero-posterior axis of the embryonic body. Hox expression is activated in the hindbrain neuroepithelium before segmentation, in response to inductive signals such as retinoic acid, and maintained through later developmental stages in neuronal progenitors and some postmitotic neurons. Analysis of loss– and gain–of–function mutations in mouse and chick embryos revealed an important role for Hox genes in the establishment of rhombomeric territories, the assignment of segmental identities, and rhombomere-specific neuronal patterns eventually required for a normal breathing behaviour at birth. The presentation will address whether and how the rhombomeric organisation of the hindbrain neural tube influences later function of respiratory control networks in chicks and mice. This involves “gene to behaviour” strategies combining studies in embryos and analysis of transgenic models. Life-threatening deficiency of a central respiratory rhythm promoting system has been first described in Krox-20-/- and Hoxa1-/- mice in which progenitor cells are mis-specified during early development [2]. In the absence of Hoxa1, some neural precursors at the presumptive r3–r4 levels fail to activate or properly maintain their appropriate molecular programs and many cells deriving from r4 are eliminated. The Krox20 gene product in r3 acts as a direct transcriptional inhibitor of r4-related Hox and participates in the formation of r3 and the r3/r4 boundary. Interestingly, r3 displays a marked delay compared with r4, in the timing of neuronal differentiation and axonal outgrowth. Therefore, heterochrony of neurogenic processes allows neuronal differentiation in r4 and continuing expression of segmental genes such as Krox20 in r3 at the same developmental stage. Given that rhombomeric heterochrony is found in both chick and mouse, we hypothesize that there are likely to be conserved signaling interactions by which the expression of Krox20 in r3 may influence neural circuits developing in r4. We are currently using chick embryological approach to investigate these signaling interactions [1,3]. Respiratory consequences of the mis-specification of r3 and r4 in mutant mice showed that Krox20 influence on r4 is of vital physiological significance in mice during the first days after birth. An “anti-apneic” neuronal system has been located in the r4-derived (“para-facial”) caudal pontine reticular formation, ventral to the facial motor nucleus (another r4-derived structure) [2]. In vivo, neonatal mice with impaired anti-apneic (para-facial) function show an abnormally low respiratory frequency and apnoeas lasting 10-times longer than normal. Most of the animals die during the first two days after birth. Rhombomere r3 is important as a source of Krox20, that is crucial to initiate parafacial development [3]. Current studies with calcium imaging of rhythm generators in mice also show that the parafacial control is embryologically distinct from the post-otic (pre-Bötzinger) respiratory generator originating caudal to r54. Finally, genetic abnormalities affecting rhombomeres rostral to r3 can lead to pontine defects, in which the respiratory frequency is not significantly affected. Altogether, data in mutant mice therefore identify a dual (parafacial and post-otic) brainstem control of the breathing rhythm.