The ZNF9 gene on chromosome 3 encodes the cellular nucleic acid binding protein (CNBP), a ubiquitously expressed, 177 amino acid (≈19.5kDa) protein that is highly conserved among vertebrates. The function of the protein is largely unknown, however an expansion in the first intron of the protein results in myotonic dystrophy type 2 (DM2), a multisystemic disease featuring cardiac arrhythmia, muscle wasting, cataracts, and a range of neuropathologies. Remarkably, we recently discovered that CNBP is involved in regulating the activity of β-secretase, the enzyme that produces the first cleavage event in the generation of the amyloid-β peptide (Aβ). The progressive fibrillization and deposition of Aβ is widely believed to be the primary causal factor in the development of Alzheimer’s disease (AD), and AD-like pathology in individuals with Down syndrome (DS). DS provides a unique model for evaluating how these factors change in the aged brain as compared to young brain, and how such changes affect the proportion of DS patients with AD. In the AD brain, both BACE1 and BACE2 increased from an early stage of disease; in DS brains, BACE1 significantly decreased (p<0.04) with age, whereas BACE2 was unchanged, even though the gene for BACE2 is located within the DS obligate region of chromosome 21. BACE1 and BACE2 activity levels were highly correlated in this series (r2 = 0.95), indicating that there may be a higher degree of shared regulation than previously believed. This implicates regulators of BACE as potentially critical for the development of AD, and our data suggests that CNBP may be one such regulator. In AD, CNBP increases early in the disease process, a change that does not occur in the normal aging process or in DS. CNBP and BACE protein levels were correlated in these cases (p<0.001), while there was no relationship between CNBP and age, or CNBP and Aβ, in either the human or mouse brain, indicating that CNBP does not increase as a consequence of normal aging. Thirty day overexpression of CNBP following adeno-associated viral delivery in murine gastrocnemius muscle resulted in an increase in BACE1 protein (p<0.01) and a consequential increase in Aβ production (p<0.01). Other experiments indicated that CNBP overexpression did not affect the half-life of BACE1 mRNA or protein, but resulted in an increase in BACE1 translation. These data indicate that CNBP is an important regulator of β-secretase, and may play an important role in the onset and progression of AD.