The amygdala is implicated in the pathophysiology of schizophrenia through its function in the processing of emotions. However, the genes involved in the dysfunction of the amygdala in schizophrenia are yet to be identified. This study examined gene expression in the amygdala in postmortem tissue from seven matched pairs of schizophrenia and non-psychiatric control subjects, using oligonucleotide-microarrays representing 19,000 gene transcripts and real-time PCR confirmation of gene expression changes in eleven matched pairs. Genes involved in presynaptic function, myelination and cellular signalling were identified as being consistently dysregulated in this cohort of subjects with schizophrenia. In particular, the expression of three genes involved in the cytomatrix active zone, Regulating membrane exocytosis 2, Regulating membrane exocytosis 3 and Piccolo, was up-regulated. These results implicate for the first time the dysfunction of the cytomatrix active zone of synapses in the amygdala in the pathophysiology of schizophrenia.