Recent evidence suggests involvement of biometal homeostasis in the pathological mechanisms in Alzheimer's disease (AD). For example, increased intracellular copper or zinc has been linked to a reduction in secreted levels of the AD-causing amyloid- peptide (A). However, little is known about whether these biometals modulate the generation of A. In the present study we demonstrate in both cell-free and cell-based assays that zinc and copper regulate A production by distinct molecular mechanisms affecting the processing by -secretase of its A precursor protein substrate APP-C99. We found that Zn2+ induces APP-C99 dimerization, which prevents its cleavage by -secretase and A production, with an IC50 value of 15 m. Importantly, at this concentration, Zn2+ also drastically raised the production of the aggregation-prone A43 found in the senile plaques of AD brains and elevated the A43:A40 ratio, a promising biomarker for neurotoxicity and AD. We further demonstrate that the APP-C99 histidine residues His-6, His-13, and His-14 control the Zn2+-dependent APP-C99 dimerization and inhibition of A production, whereas the increased A43:A40 ratio is substrate dimerization-independent and involves the known Zn2+ binding lysine Lys-28 residue that orientates the APP-C99 transmembrane domain within the lipid bilayer. Unlike zinc, copper inhibited A production by directly targeting the subunits presenilin and nicastrin in the -secretase complex. Altogether, our data demonstrate that zinc and copper differentially modulate A production. They further suggest that dimerization of APP-C99 or the specific targeting of individual residues regulating the production of the long, toxic A species, may offer two therapeutic strategies for preventing AD.