Background: The mitochondrial membrane potential (Delta Psi(m)) controls the generation of adenosine triphosphate (ATP) and reactive oxygen species, and sequesteration of intracellular Ca2+[Ca2+](i). Clinical concentrations of sevoflurane affect the Delta Psi(m) in neural mitochondria, but the mechanisms remain elusive. The aim of the present study was to compare the effect of isoflurane and sevoflurane on Delta Psi(m) in rat pre-synaptic terminals (synaptosomes), and to investigate whether these agents affect Delta Psi(m) by inhibiting the respiratory chain. Methods: Synaptosomes were loaded with the fluorescent probes JC-1 (Delta Psi(m)) and Fura-2 ([Ca2+](i)) and exposed to isoflurane or sevoflurane. The effect of the anaesthetics on the electron transport chain was investigated by blocking complex I and complex V. Results: Isoflurane 1 and 2 minimum alveolar concentration (MAC) decreased the normalized JC-1 ratio from 0.92 +/- 0.03 in control to 0.86 +/- 0.02 and 0.81 +/- 0.01, respectively, reflecting a depolarization of the mitochondrial membrane (n = 9). Isoflurane 2 MAC increased [Ca2+](i). In Ca2+-depleted medium, isoflurane still decreased Delta Psi(m) while [Ca2+](i) remained unaltered. The effect of isoflurane was more pronounced than for sevoflurane. Blocking complex V of the respiratory chain enhanced the isoflurane- and sevoflurane-induced mitochondrial depolarization, whereas blocking complex I and V decreased Delta Psi(m) to the same extent in control, isoflurane and sevoflurane experiments. Conclusions: Isoflurane and sevoflurane may act as metabolic inhibitors by depolarizing pre-synaptic mitochondria through inhibition of the electron transport chain, although isoflurane seems to inhibit mitochondrial function more significantly than sevoflurane. Both agents inhibit the respiratory chain sufficiently to cause ATP synthase reversal.