Ischemic tolerance in the brain, in which sub-threshold insults increase resistance to subsequent injurious ischemia, is a powerful adaptive defense that involves an endogenous program of neuroprotection. Emerging evidence from genomic studies suggests diverse stimuli that trigger preconditioning achieve neuroprotection through a common process which depends on a fundamental reprogramming of the response to injury. Such reprogramming of the genomic response to injury leads to the induction of novel neuroprotective pathways not ordinarily found in the setting of ischemia. Genomic studies also indicate that the nature of the preconditioning stimulus (eg, brief ischemia or endotoxin [lipopolysaccharide]) dictates the phenotype of neuroprotection, a phenotype that parallels protective adaptations also found in certain physiological conditions where the preconditioning stimulus exists at levels that can induce injury. The idea that preconditioning leads to a fundamental reprogramming event that confers neuroprotection is a novel and important concept in the field of ischemic tolerance. Moreover, the view that distinct preconditioning stimuli confer neuroprotection via effectors that differ according to the nature of the preconditioning stimulus offers promise that multiple, nonoverlapping pathways may be discovered as novel neuroprotective therapies.