The accumulation of the amyloid-β (Aβ) peptide in the form of insoluble fibrillar deposits and soluble oligomeric aggregates is widely believed to play a causal role in Alzheimer’s disease (AD). Proteolytic cleavage of APP by the β-site APP cleaving enzyme (BACE1) near the C-terminus results in the formation of the APP C-terminal fragment (CTF) C99, a substrate for subsequent cleavage by γ-secretase to generate Aβ. Alternatively, APP cleavage by α-secretase to generate the APP CTF C83 occurs within the Aβ region, precluding its formation. Therefore, modulation of β- and/or γ-secretase activity represents important therapeutic targets. Transgenic mice overexpressing human APP generate detectable levels of APP CTFs and Aβ. We have shown that highly sensitive and specific methods for determining levels of APP CTFs and Aβ are useful for understanding how genetic manipulation of APP processing impacts Aβ generation and accumulation.