Schizophrenia is a complex psychiatric disorder, affecting 1% of the population. It is a multifactorial disease characterised by positive symptoms, negative symptoms and cognitive deficits. The cognitive deficits (impaired working memory, attentional and executive function deficits) are considered a core feature resulting primarily from dysfunction in the prefrontal cortex. Despite concerted efforts into the cause of schizophrenia, the genetic components of this complex disease remain elusive. We performed a global transcriptome screen to identify schizophrenia-associated genes differentially expressed in the prefrontal cortex, utilising a phencyclidine (PCP) rat model of schizophrenia (Cochran et al 2003) and rat oligonucleotide GeneChips from Affymetrix. This PCP treatment regime developed in our laboratories produces a pattern of metabolic hypofunction, neurochemical changes and cognitive deficits in the rodent brain that closely mirror those observed in the brains of schizophrenic patients (Cochran et al 2003 and Morris et al 2005) 327 differentially expressed transcripts were identified. Many of the associated genes map to key schizophrenia loci, including the neurodevelopmental gene DPYSL2 that maps to 8p21-22 and has been previously implicated as a susceptibility gene for schizophrenia and the AMPA receptor subunit gene GRIA1 (GluR1) that maps to SCZD1 (schizophrenia susceptibility locus 1) on 5q33. We present the microarray identification of schizophrenia-associated genes and confirmatory real-time PCR data on differentially expressed genes mapping to key schizophrenia loci. We conclude that microarray analysis of a validated animal model of prefrontal cortex deficits in schizophrenia can lead to the identification of genes involved in the cognitive aspects of the disease. This approach has identified genes previously linked to schizophrenia together with novel genes that may represent a completely novel convergent pathway underlying the cognitive deficits associated with schizophrenia. Together these findings have implications for novel drug target development.