Transposable elements (TEs) are active in neuronal cells raising the question whether TE insertions contribute to risk of neuropsychiatric disease. While genome‐wide association studies (GWAS) serve as a tool to discover genetic loci associated with neuropsychiatric diseases, unfortunately GWAS do not directly detect structural variants such as TEs. To examine the role of TEs in psychiatric and neurologic disease, we evaluated 17,000 polymorphic TEs and find 76 are in linkage disequilibrium with disease haplotypes (P < 10−6) defined by GWAS. From these 76 polymorphic TEs, we identify potentially causal candidates based on having insertions in genomic regions of regulatory chromatin and on having associations with altered gene expression in brain tissues. We show that lead candidate insertions have regulatory effects on gene expression in human neural stem cells altering the activity of a minimal promoter. Taken together, we identify 10 polymorphic TE insertions that are potential candidates on par with other variants for having a causal role in neurologic and psychiatric disorders. Synopsis This study reviews 17,000 polymorphic transposable elements and identifies insertions genetically associated with neuropsychiatric disorders. Features of lead examples are on par with other variants for having a causal role in neurologic and psychiatric disorders. We identify polymorphic transposable elements that are genetically linked to risk of neuropsychiatric disorders. Lead transposable element insertions have regulatory activity in a promoter assay tested in human neural stem cells. Polymorphic transposable elements are associated with altered expression of potential disease genes in neurologic tissues. This study reviews 17,000 polymorphic transposable elements and identifies insertions genetically associated with neuropsychiatric disorders. Features of lead examples are on par with other variants for having a causal role in neurologic and psychiatric disorders.