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The CompacT SelecT is the latest generation automated cell culture system in the SelecT product line allowing incubation of up to 90 T-175 flasks and preparation of 210 assay-ready plates. We have successfully implemented the CompacT SelecT in support of a number of cell-based assays used in our Alzheimer's disease (AD) lead optimization programs. One of the distinguishing features of AD pathology is deposition of two neurotoxic forms of the beta-amyloid peptide (Aβ40and Aβ42) in the brains of patients. It is thought that specifically lowering Aβ40and Aβ42in the brains of patients will halt the progression of the disease. The generation of Aβ requires sequential cleavage of the type-I integral membrane amyloid precursor protein (APP) by two proteases, β-secretase (BACE) then γ-secretase. In the specific examples presented here, we have transitioned two cell lines supporting drug discovery efforts for identifying β- and γ-secretase inhibitors (GSIs) from manual cell culture protocols to fully automation using CompacT SelecT. In Chinese hamster ovary (CHO) cells which over express wild-type APP (CHOAPPcells), robust secretion of Aβ40was observed from cells cultured manually and with CompacT SelecT with signal:background ratios of 54–99 and 23–47, respectively. Despite the reduced signal:background observed with the CompacT SelecT cultured cells, the rank order of potency for a series of 18 BACE inhibitors in reducing Aβ40secretion was identical when manually cultured cells were compared with CompacT SelecT cultured cells. The correlation coefficient when comparing the two sets of EC50values was r2= 0.99. Similarly, CHO cells that over express a reporter construct for the Swedish mutant APP that generates high levels of Aβ peptide (CHOAPP-NLcells) cultured with CompacT SelecT exhibited a reduced secretion of Aβ40and Aβ42when compared with manually cultured cells; signal:background ratios for secretion of Aβ40from CHOAPP-NLcells were 57–71 and 16–31, and for Aβ42secretion 8–18 and 4–11 comparing manual and automated cell culture, respectively. Similar to the observations in CHOAPPcells, an identical rank order of potency for a series of GSIs was observed when CHOAPP-NLcells cultured manually and in CompacT SelecT were compared; r2= 0.99 and 0.98, respectively, for EC50values for inhibition of Aβ40and Aβ42secretion. Taken together, the robust signal:background and identical pharmacological profile of inhibitors provide validation for the implementation of automated cell culture for CHOAPPand CHOAPP-NLcells in support of β- and γ-secretase-targeted drug discovery.