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Abstract Altered arginine metabolism has been implicated in the pathogenesis of schizophrenia. The present study measured the levels of L-arginine and its downstream metabolites in the sub-regions of the hippocampus, prefrontal cortex and cerebellum in adult rats that had been exposed to maternal immune activation (MIA; a risk factor for schizophrenia). MIA significantly increased L-arginine, L-ornithine and putrescine levels and decreased agmatine levels in the hippocampus and prefrontal cortex in a region-specific manner. Correlational analysis revealed a significant neurochemical–behavioural correlation. Cluster analyses showed that L-arginine and its main metabolites formed distinct groups, which changed as a function of MIA. These results demonstrate, for the first time, that MIA leads to altered arginine metabolism in the hippocampus and prefrontal cortex of the adult offspring.