Rat genome U34A (Affymetrix®) oligonucleotide microarrays were used to analyze changes in gene expression in the caudate putamen (CPu) of Fischer rats induced by 1 and 3 days of “binge” cocaine (or saline) administration. A triplicate array assay of pooled RNA of each treatment group was used to evaluate the technical variability and sensitivity of microarrays. Cocaine‐regulated genes were identified using the Affymetrix MAS 5.0 and Data Mining Tool v. 3. Eighty‐nine upregulated and eight downregulated genes/ESTs were found after 1 day of “binge” cocaine. Following 3 days of cocaine treatment we identified 21 upregulated and 17 downregulated genes/ESTs. RNase protection assays of selected genes confirmed reliability of changes identified by the microarrays at the level of ≥1.40‐fold increase. Many genes upregulated in the CPu by cocaine were immediate early genes for transcription factors and for “effector” proteins (e.g., vesl/Homer1a, Arc, synaptotagmin IV). Acute “binge” cocaine also increased mRNA levels for glutamate receptor GluR2, dopamine receptor D1, and a number of phosphatases. Genes downregulated by cocaine include several genes associated with energy metabolism in mitochondria, as well as the phosphatydylinositol‐4 kinase and the regulator of G‐protein signaling protein 4 (RGS4). A differential expression of somatostatin receptor SSTR2, not known to be a cocaine‐responsive gene, as well as the clock gene Per2, were found by microarrays and confirmed by RNase protection assay. These results demonstrate the potential of microarrays in profiling gene expression with ≥40% increase or ≥14% decrease in mRNA levels for discovery of novel cocaine‐responsive genes. Synapse 48:157–169, 2003. © 2003 Wiley‐Liss, Inc.