c-Jun N-terminal kinases (JNKs), a family of MAP kinases, are central mediators of apoptosis and neurodegeneration, but also of plasticity and regeneration. Current concepts suggest that the compartmentalisation i.e. the distribution within cellular organelles and structures rather than substrate affinity determines the pathological and physiological function of individual JNKs. In contrast to JNK mediated activation of pro-apoptotic Bcl-2/BH3-only substrates, findings on the presence and activation of JNK isoforms in mitochondria are rare. Here we have analysed the specific localisation and activation of JNK1, JNK2 and JNK3 as well as of their upstream MKK4/7 in brain mitochondria following transient middle cerebral artery occlusion (MCAo). The mitochondrial preparations were free of cytoskeletal, nuclear and ER contaminations, the specificity of antibodies was demonstrated in brain mitochondria from JNK deficient untreated mice. All JNKs were present in mitochondria with JNK1 as the major carrier of a strong basal JNK activity. Surprisingly, JNK activity was hardly detectable in the remaining cytoplasm. Between 2 and 18 h following MCAo, the pattern of JNK isoforms in mitochondria completely changed. Presence and activation of JNK1 almost completely disappeared. In striking contrast, presence and activation of JNK2 and, even more pronounced, of JNK3 substantially increased. At the level of the upstream MKKs, complexes of MKK4:JNK1 were diminished, whereas complexes of JNK3 with MKK4 and MKK7 were enhanced. These data strongly suggest that the basal physiological JNK1 activity is replaced in mitochondria by activated JNK2 and JNK3 following neurodegenerative events. This pattern of “JNK1 goes and JNK3 comes” might be essential for the initiation of apoptosis and suggests the search for targets of compartment-specific neuroprotective strategies.