It has been suggested that the antibiotic minocycline (MC) acts as a neuroprotectant by inhibiting the mitochondrial permeability transition pore (Zhu S et al., 2002, Nature 417, 74). Though we are able to show such an inhibiting effect of MC under some conditions, this view was questioned by a multicentre, randomised placebo-controlled phase III trial recently showing that MC has harmful effects on ALS patients (Gordon PH et al., 2007, Lancet Neurol. 6, 1045). To understand these contradictory results the effects of MC on freshly prepared rat liver mitochondria and on mitoplasts were studied. Mitochondria were suspended either in a KCl-based medium (125 mM KCl, 20 mM Tris, 1 mM EGTA, 5 mM glutamate, 5 mM malate, and 1 mM Pi; pH 7.2) or in a sucrose-based medium (200 mM sucrose, 10 mM Tris, 1 mM KH₂PO₄, 10 mM EGTA, 5 mM glutamate and 5 mM malate; pH 7.2). It turned out that MC exerts strong detrimental effects on the Ca²⁺-retention capacity, on the membrane potential, and on the ADP-/FCCP-stimulated respiration of RLM incubated in KCl-based medium. Additionally, we observed cytochrome c release and swelling of the mitochondria. The effects were weaker or absent when the mitochondria were bathed in a sucrose-based medium. We explain our results by an increased permeability of the inner membrane to ions of low molecular weight like NADH, Mg²⁺, K⁺, and Cl^-. As the flow of K⁺ and Cl^- can be inhibited by dicyclocarbodiimide and by tributyltin and as MC binds Mg²⁺ very effectively, we assume that a reduced Mg²⁺-concentration activates the K⁺-uniport, the Inner Mitochondrial Anion Channel (IMAC, a 108 pS-Cl-channel), and very likely a further large-conductance channel. In conclusion, MC has beneficial as well as detrimental effects on mitochondria. The detrimental effects, however, seem to be predominant.