In the 50 years since APOE was identified, fundamental discoveries about the structure and function of its three isoforms—APOE2, APOE3, and APOE4—have elucidated their roles in cardiovascular and neurological diseases. Although these isoforms differ by only a single amino acid, APOE2 and APOE4 differ profoundly in structure and function from APOE3, the most common isoform. APOE2 is associated with type III hyperlipoproteinemia, which causes atherosclerosis due to plasma lipoprotein accumulation, specifically chylomicron and very-low-density lipoprotein remnants. Cysteine-158 in APOE2 alters the conformation of the region that binds to lipoprotein receptors and heparan sulfate proteoglycans (HSPG) (residues 136–150), reducing binding affinity. Other amino acid changes in this region of APOE result in dominant versus recessive hyperlipidemia and shed light on the importance of cell-surface HSGP binding for uptake of APOE-containing lipoproteins and tau. APOE4 is the major genetic risk factor for Alzheimer’s disease and likely the major causative factor. Neurons synthesize APOE in response to stress. Owing to the unique structure of APOE4, with arginine at residue 112, arginine-61 in the amino-terminal domain interacts with glutamic acid-255 in the carboxyl-terminal domain. Domain interaction is associated with neuron-specific proteolysis, which generates neurotoxic fragments that cause cytoskeletal alterations (e.g., hyperphosphorylation of tau) and mitochondrial dysfunction, which are associated with the loss of hippocampal GABAergic inhibitory interneurons and cognitive impairment. Understanding the structural features of the APOE isoforms opens new avenues for modulating their effects in cardiovascular and neurological diseases, including gene therapy, decreasing APOE4 expression, inhibiting neuron-specific proteolysis, replacing lost GABAergic interneurons by hippocampal transplantation, and administering mitochondrial protectors.