The Na+/H+ exchangers (NHEs) are a family of antiporters involved in the maintenance of neural steady-state intracellular pH. The NHE3 seems to be the predominant subtype in central chemosensitive cells. We aimed to analyze the effect of a selective NHE3 inhibition on the respiratory pattern in spontaneously breathing rats with intact vagi. Rats were intravenously infused for 10 min with the selective NHE3 inhibitor AVE1599 (Aventis Pharma Deustchland, 0.5 and 2 mg/kg) or with phosphate buffer. Whole-body plethysmography was used to monitor breathing pattern before, during, and up to 30 min after the drug infusion. Immunohistochemistry for the c-Fos protein was performed in the animal brains and c-Fos-positive cells were counted along the brainstem. Selective NHE3 inhibition induced a significant increase in the respiratory frequency and in the number of c-Fos immunopositive cells in the lateral parabrachial nucleus, the pre-Bötzinger complex and a rostral extension of the retrotrapezoid nucleus/parapyramidal region (p<0.05, ANOVA). We conclude that systemic administration of AVE1599 increases respiratory frequency and activates ponto-medullary areas implicated in the central control of breathing and chemoreception.