Transient cerebral ischemia leads to protein aggregation mainly in neurons destined to undergo delayed neuronal death after ischemia. This study utilized a rat transient cerebral ischemia model to investigate whether ischemic preconditioning is able to alleviate neuronal protein aggregation, thereby protecting neurons from ischemic neuronal damage. Ischemic preconditioning was introduced by a sublethal 3 min period of ischemia followed by 48 h of recovery. Brains from rats with either ischemic preconditioning or sham-surgery were then subjected to a subsequent 7 min period of ischemia followed by 30 min, 4, 24, 48 and 72 h of reperfusion. Protein aggregation and neuronal death were studied by electron and confocal microscopy, as well as by biochemical analyses. Seven minutes of cerebral ischemia alone induced severe protein aggregation after 4 h of reperfusion mainly in CA1 neurons destined to undergo delayed neuronal death (which took place after 72 h of reperfusion). Ischemic preconditioning reduced significantly protein aggregation and virtually eliminated neuronal death in CA1 neurons. Biochemical analyses revealed that ischemic preconditioning decreased accumulation of ubiquitin-conjugated proteins (ubi-proteins) and reduced free ubiquitin depletion after brain ischemia. Furthermore, ischemic preconditioning also reduced redistribution of heat shock cognate protein 70 and Hdj1 from cytosolic fraction to protein aggregate-containing fraction after brain ischemia. These results suggest that ischemic preconditioning decreases protein aggregation after brain ischemia. Keywords brain ischemia; preconditioning; protein aggregation; proteotoxicity; electron microscopy A brief episode of cerebral ischemia followed by reperfusion leads to delayed neuronal death in CA1 neurons at 48-72 h of reperfusion, while leaving dentate gyrus (DG), CA3 and most cortical neurons largely intact (Ito et al., 1975;Kirino, 1982;Smith et al., 1984). During this delayed period, neurons destined to undergo delayed neuronal death look normal under light microscopy. Under electron microscopy (EM), however, these CA1 neurons contain large quantities of intracellular protein aggregates (Hu et al., 2000).Cellular proteins in non-native states, i.e. unfolded (newly synthesized), misfolded, denatured, or damaged, expose the sticky hydrophobic segments, and are highly toxic to cells (Taylor et al., 2002;Dobson, 2003). There are several cellular defense systems to process proteins in non-native states and to reduce their proteotoxicity (Dobson, 2003 Proteasomal degradation of ubiquitin-conjugated proteins (ubi-proteins) is also strictly ATPdependent. Brain ischemia depletes ATP and changes intracellular homeostasis, thereby disabling ATP-dependent molecular chaperones and ubiquitin-proteasomal degradation, resulting in toxic aggregation of non-native proteins during the postischemic phase (Hu et al., 2000(Hu et al., , 2001.A short period of ischemia (ischemic preconditioning) that does not lead to neuronal death (sublethal), is able to i...