Genomic DNA in the brain can acquire somatic genetic variations by retrotransposition. The authors found higher copy numbers of the retrotransposon L1 in the prefrontal cortex of patients with schizophrenia. Whole-genome sequencing of brain tissue revealed L1 insertion in or near genes associated with synapse function and schizophrenia. Furthermore, in a mouse model of environmentally induced immune activation, brain genomic DNA showed higher L1 copy numbers. These findings suggest that increased L1 retrotransposition in neurons, triggered by environmental and/or genetic risk factors, may contribute to schizophrenia susceptibility and pathophysiology.