Variation at the APOE gene locus has been shown to affect the risk for Alzheimer's disease. To gain deeper insight into the postulated apoE-mediated amyloid formation, we have characterized the three common apoE isoforms (apoE2, apoE3, and apoE4) regarding their binding to amyloid precursor protein (APP). We employed the yeast two-hybrid system and co-immunoprecipitation experiments in cell culture supernatants of COS-1 cells, ectopically expressing apoE isoforms and APP751 holoprotein or a COOH-terminal Abeta deletion mutant protein, designated APPtrunc. We found that all three apoE isoforms were able to bind APP751 holoprotein in an Abeta-independent fashion. The interacting domains could be mapped to the NH2 termini of APP (amino acids 1-207) and apoE (amino acids 1-191). As a functional consequence of this novel APP751 ectodomain-mediated apoE binding, the secretion of soluble APP751 is differentially affected by distinct apoE isoforms in vitro, suggesting a new "chaperon-like" mechanism by which apoE isoforms may modulate APP metabolism and consequently the risk for Alzheimer's disease.