The use of DNA arrays offers the promise of semiquantitative analysis of large numbers of genes simultaneously. Here, we report our efforts at applying this technology to an issue of potentially high relevance to current research in Alzheimer’s Disease (AD). The AD field is in strong need of biomarkers suitable for the diagnosis of AD prior to symptomology. Amyloid-beta (Aβ) deposition in the brain is a hallmark of AD, and amino acid racemization studies suggest that Aβ deposition occurs well before symptomology (1). Hence, approaches that provide an indirect indication of Aβ burden may be useful in early AD diagnosis. A mouse model of Aβ deposition resulting from overexpression of the Aβ protein precursor has proven utility as a model of AD. Although such mice do not have the striking neuronal loss seen in AD, these mice manifest many of the other attributes of AD including fibrillar and nonfibrillar Aβ deposits, neuritic plaques, decreased synapse density and gliosis, and behavior problems (2–4). Moreover, they have proven useful in studies aimed at decreasing Aβ deposition, e.g., the Aβ vaccination studies (5–7). As a means to identify markers of Aβ deposition that may prove useful in diagnosing AD before symptomology and in assessing decreases in Aβ burden with therapy, we attempted to use cDNA array technology to identify patterns of altered gene expression in Aβ-overexpressing mice. This chapter documents our efforts at the analysis, interpretation, and confirmation of these efforts.