There are three major apolipoprotein E (apoE) isoforms. Whereas APOE-e3 is considered as a longevity gene, APOE-e4 is a dual risk factor to atherosclerosis and Alzheimer’s disease. We have expressed full-length and N- and C-terminal truncated apoE3 and apoE4 tailored to eliminate helix- and domain interactions to unveil structural and functional disturbances. The N-terminal truncated apoE472-299 and C-terminal truncated apoE41-231 showed more complicated or aggregated species than those of the corresponding apoE3 counterparts. This isoformic structural variation did not exist in the presence of dihexanoylphosphatidylcholine. The C-terminal truncated apoE1-191 and apoE1-231 proteins greatly lost the lipid-binding ability as illustrated by the dimyristoylphosphatidylcholine turbidity clearance. The LDL receptor-binding ability, determined by a competition binding assay of 3H-LDL to LDL-receptor of HepG2 cells, showed that apoE4 proteins with N- (apoE472-299), C-terminus (apoE41-231), or complete C-terminus truncation (apoE41-191) maintained greater receptor-binding abilities than their apoE3 counterparts. The cholesterol-lowering abilities of apoE372-299 and apoE31-231 in apoE-deficient mice were decreased significantly. The structural preference of apoE4 to remain functional in solution may explain the enhanced opportunity of apoE4 isoform to display its pathophysiologic functions in atherosclerosis and Alzheimer’s disease.