Bicarbonate transport (BT) has been previously shown to modulate the ischemia-induced apoptosis. To understand the underlying cellular mechanisms of bicarbonate-dependent apoptosis and find out which specific transporter may be involved was the aim of the present study. For this purpose rat coronary endothelial cells (EC) were exposed to simulated ischemia (glucose free anoxia at pH 6.4) for 2 hours. Simulated ischemia in bicarbonate-buffered medium increased caspase-3 activity and the number of apoptotic cells (21.2+1.4% vs. 5.1+1.2% in control). Omission of bicarbonate (HEPES-buffer), i.e. suppression of all bicarbonate-dependent transporter, during ischemia further significantly increased caspase-3 activity and the number of apoptotic cells (36.7+1.7). RT-PCR- and western blot analyses of SLC4-family bicarbonate-dependent transporters revealed a pronounced expression of SLC4A7 transporter, i.e. electroneutral sodium-bicarbonate co-transporter (NBCn1). To examine the role of NBCn1 in ischemia-induced apoptosis EC were treated with the specific inhibitor S0859 (1 mmol/l, Sanofi-Aventis) in a bicarbonate-buffered medium. Similarly to omission of bicarbonate, treatment with S0859 increased the caspase-3-activity and elevated the number of apoptotic cells, whereas no effect could be observed in non-ischemic EC. Analysis of the underlying cellular mechanisms of NBCn1-dependent apoptosis revealed activation of the mitochondrial pathway of apoptosis, i.e. increase of mitochondrial cytochrome-C-release and cleavage of caspase-9, under S0859 treatment. In contrast, no activation of endoplasmic reticulum-dependent pathway (caspase-12-cleavage) or extrinsic apoptotic pathway (caspase-8-cleavage) was detected. Therefore, NBCn1 is an important modulator of the mitochondrial pathway of apoptosis in ischemic coronary EC.