Amyloid-beta peptide aggregation is a signature of Alzheimer disease and a frequent complication of adult Down syndrome patients. Amyloid-beta is generated by proteolytic processing of the amyloid precursor protein (APP) by beta- and gamma-secretase at the N and C termini, respectively. Presenilin-1 is involved in the gamma-secretase activity. BACE is a transmembrane aspartyl protease with beta-secretase activity. BACE2, also termed ALP56 has 2 pepsin-like active centers, a signal sequence, a propeptide, and a long C-terminal extension including a transmembrane domain, with expression in a wide array of tissues. Northern blot analysis revealed low expression of 2.0- and 2.6-kb BACE2 transcripts in most fetal and adult tissues, with higher expression in adult colon, kidney, pancreas, placenta, prostate, stomach, and trachea. Low levels were also detected in brain, with somewhat higher expression in medulla and spinal cord. In situ hybridization analysis of rat brain found low-level BACE2 expression in contrast to BACE expression. The BACE2 expression pattern does not appear to be consistent with that of a beta-secretase. BACE2 has been mapped to 21q22.3, within the Down syndrome critical region.