In addition to 2',7'-bis-(2-carboxyethyl)-5(6)- carboxyfluorescein (BCECF) used so far to monitor intramitochondrial pH, two other fluorescent pH indicators, 4',5'-dimethyl-5(6)-carboxyfluorescein (DMCF) and carboxyseminaphthofluorescein (carboxy-SNAFL-1), were applied for this purpose. These probes are taken up by isolated rat liver mitochondria in form of diacetate esters, hydrolyzed within mitochondria to free acids, and respond to changes of intramitochondrial pH by changing their fluorescence emission intensity. With all three probes energization of mitochondria by electron donors or acceptors was accompanied by fluorescence changes characteristic for alkalization, whereas deenergization by respiratory inhibitors or protonophores produced changes typical for acidification. Contrary to this, transition from State 4 to State 3, known to shift intramitochondrial pH towards acidification (equivalent to a decrease of ApH), was accompanied by paradoxical responses of the fluorescent pH probes used: the fluorescence of DMCF increased as if the matrix compartment became more alkaline, the fluorescence of BCECF, measured in single excitation/emission wavelength mode, did not change, and the fluorescence of carboxy-SNAFL-1 could be interpreted as either alkalization or acidification, depending on the excitation/emission wavelength pair used. It was shown that depletion of intramitochondrial Mg2+ and Ca2+ using divalent metal ionophore A23187 decreased fluorescence intensity with all three probes examined, whereas subsequent addition of Mg2+ or Ca2+ increased the fluorescence. It is therefore proposed that the atypical response of intramitochondrial pH indicators upon State 4 - State 3 transition is due to changes of intramitochondrial free Mg2+, as related to different complexing abilities of ATP and ADP towards magnesium.