When running in vivo experiments it is imperative to keep arterial blood pressure and acid-base parameters within the normal physiological range. The aim of this investigation was to explore the consequences of anesthesia-induced acidosis on basal and PGE₂-stimulated duodenal bicarbonate secretion. Mice (strain C57bl/6J) were kept anesthetized by spontaneous inhalation of isoflurane. Mean arterial blood pressure (MAP), arterial acid-base balance and duodenal mucosal bicarbonate secretion (DMBS) were studied. Two intra-arterial fluid support strategies were used; a standard Ringer solution and isotonic sodium carbonate solution. Duodenal single perfusion was used and DMBS was assessed by back titration of the effluent. Prostaglandin E₂ (PGE₂) was used to stimulate DMBS. In Ringer-infused mice, isoflurane induced acidosis became worse with time. Blood pH was 7.15-7.21 and base excess about -8 mM at the end of experiments. Continuous infusion of Na₂CO₃ completely compensated for the acidosis. Blood pH was 7.36-7.37 and base excess about 1 mM at the end of the experiment. Basal and PGE₂-stimulated DMBS were markedly greater in animals treated with sodium carbonate than in those treated with Ringer. MAP was slightly higher after Na₂CO₃-infusion than after Ringer-infusion. It is concluded that isoflurane-induced acidosis markedly depresses basal and PGE₂-stimulated DMBS, as well as the responsiveness to PGE₂, effects prevented by continuous infusion of Na₂CO₃. When performing in vivo experiments in isoflurane-anaesthetized mice, it is recommended to supplement with sodium carbonate-infusion to maintain normal acid-base balance.