This transcriptome-wide reference map of RNA splicing in the aging cortex is a new resource that highlights strong effects of neuropathology and genetic variation on splicing. It will be useful in annotating the results of genetic and epigenomic studies of neurologic and psychiatric diseases, but it has an immediate impact in (1) identifying the functional consequences of several Alzheimer’s disease susceptibility alleles, (2) extending the list of loci involved in Alzheimer’s disease, and (3) implicating the protein degradation machinery in the pathology of Alzheimer’s disease.