Rationale: The sodium/proton exchanger NHE3 is expressed in brainstem areas with prevalence for central chemosensitivity. Selective NHE3 inhibitors can evoke CO₂ mimetic responses both in vitro and in vivo, demonstrating the functional significance of this pH regulating protein. Moreover, levels of NHE3 expression are inversely correlated to inter-individual differences of base-line ventilation in conscious rabbits. Objectives: Now we explored the influence of chronic acid-base disturbances on mRNA levels of brainstem NHE3 in relation to breathing control. Methods: Alveolar ventilation (V_A), blood gases, systemic base excess (BE) and metabolic CO₂-production (VCO₂), were determined in rabbits shortly after exposure to either CO₂-enriched air for three days (N=5) or to ammonium chloride with the drinking water for two days (N=6). Untreated animals served as controls (N=24). NHE3 mRNA within the obex region was quantified by realtime RT-PCR. Results: After chronic hypercapnia, we found a compensatory rise of BE (mean±SEM) to 5.3±0.5 mmol[[rad]]l^-1 with slightly elevated PaCO₂. Brainstem NHE3 mRNA as well as V_A were not significantly different from control levels. In the NH₄Cl group, arterial pH was ~0.09 units lower than control and BE decreased to -6.5±1.6 mmol[[rad]]l^-1 with slightly decreased PaCO₂, but considerably reduced V_A (by~25%, P<0.05) and VCO₂. Concomitantly, brainstem NHE3 mRNA had increased from control level of 1.45±0.19 to 3.64±0.37 fg cDNA/µg RNA, P<0.01. Conclusions: Expression of brainstem NHE3 is up-regulated by chronic metabolic acidosis but not by prolonged hypercapnia. It is proposed that elevated brainstem NHE3 expression contributes to limit maladaptive hyperventilation during metabolic acidosis.