Septal nuclei, located in the anterior basal forebrain, exert strong control over hippocampal function and are critical for memory in animal models, yet remain understudied in humans. Until very recently, septal nuclei were not included in any of the standard neuroanatomic templates commonly used to interpret neuroimaging studies. We therefore developed and validated a new magnetic resonance imaging (MRI) manual tracing method based on direct examination of preserved human brain specimens to accurately measure this region in humans. Unexpectedly, we found robust septal enlargement in patients with temporal lobe epilepsy and healthy subjects destined to develop Alzheimer’s disease (AD) years later, suggesting plasticity/augmentation of a cholinergic septo-hippocampal system that is both antiepileptic and essential for normal memory function. Septal enlargement contrasts with atrophy in the rest of the basal forebrain, and may serve as an AD biomarker and inform understanding of AD pathogenesis.