Methamphetamine (METH) is recognized as one of the most abused psychostimulants in the USA. METH is an illicit drug that is known to exert neurotoxic effects on both dopaminergic and serotonergic neural systems. Our laboratory has been studying the biochemical mechanisms underlying MDMA and METH-induced neurotoxic effects both in vivo and in vitro. Our substance abuse research focuses on the global alteration of cortical protein expression in rats treated with acute METH. Altered protein expression was identified using a multistep protein separation/proteomic platform. Differential changes of the selected proteins were further confirmed by quantitative immunoblotting. Our study identified 82 differentially expressed proteins, 40 of which were downregulated and 42 of which were upregulated post acute METH treatment. Proteins that were shown to be downregulated included collapsin response mediator protein-2 (CRMP-2), superoxide dismutase 1 (SOD 1), and phosphatidylethanolamine-binding protein-1 (PEBP-1). Proteins that were shown to be upregulated included authophagy-linked microtubule-associated protein light chain 3 (LC3), synapsin-1, and Parkinsonism-linked ubiquitin carboxy-terminal hydroxylase-L1 (UCH-L1). This differential protein expression highlights on the neurotoxic mechanism involved in METH exposure as well as to discover potential markers for METH-induced neurotoxicity. In this chapter, we describe the current protocols for the in vivo rat model of acute METH treatment (40 mg/kg) coupled with the description of the multistep separation platform applied. These methods and protocols are discussed in the paradigm of acute model of methamphetamine drug abuse and can be applied to other models of substance abuse such as to MDMA or cocaine.