Methamphetamine (mAMPH) is a highly addictive psychostimulant drug that injures monoaminergic neurons and results in behavioral impairments in humans and animals. Although evidence exists for changes in cortical volume, metabolism, and blood oxygenation levels in human mAMPH abusers, animal models have instead emphasized this drug's long-lasting influence on ascending monoaminergic (dopamine, serotonin) projections. The aim of this study was to investigate cortical and subcortical function in rats long after administration of a single-day mAMPH regimen known to damage monoaminergic systems, at a time point when behavioral impairments are still evident. Rats were given either saline or a neurotoxic (4 × 4 mg/kg, sc) mAMPH regimen. Five weeks later, they were given pharmacological treatments that stimulate cortical gene expression: either the dopaminergic agonist apomorphine (3 mg/kg, sc) or the muscarinic acetylcholine agonist pilocarpine (25 mg/kg, ip). Cortical and subcortical immediate early gene (IEG) responses were measured by immunocytochemical analysis of Fos or JunB, protein products of the IEGs, c-fos and junB. Compared with saline-pretreated controls, mAMPH-pretreated animals had about 50–70% fewer Fos- and JunB-immunoreactive cells in anterior cingulate, infralimbic, orbital, somatosensory, and rhinal cortices as well as caudate-putamen and nucleus accumbens, 90 min after apomorphine challenge. By contrast, mAMPH-pretreated rats had no reductions in the numbers of Fos or JunB-positive cells following pilocarpine challenge. This study demonstrates the profound and enduring effects of mAMPH administration on dopamine-stimulated cortical function in animals. Synapse 63:403–412, 2009. © 2009 Wiley-Liss, Inc.