Sequential processing of the beta-amyloid precursor protein (APP) by beta- and gamma - secretase generates the amyloid beta - peptide (Abeta), which is widely believed to play a causative role in Alzheimer´s disease (AD). Selective lowering of the pathogenic 42 amino acid variant of Abeta by gamma-secretase modulators (GSMs) is a promising therapeutic strategy. Here we report that mutations in presenilin (PS), the catalytic subunit of gamma-secretase, display differential responses to nonsteroidal anti-inflammatory drug (NSAID) - type GSMs and more potent second-generation compounds. While many pathogenic PS mutations resisted lowering of Abeta42 generation by the NSAID sulindac sulfide, the potent NSAID-like second-generation compound GSM-1 was capable of lowering Abeta42 for many but not all mutants. We further found that mutations at homologous positions in PS1 and PS2 can elicit differential Abeta42 responses to GSM-1 suggesting that a positive GSM-1 response depends on the spatial environment in gamma-secretase. The aggressive pathogenic PS1 L166P mutation was one of the few pathogenic mutations that resisted GSM-1, and L166 was identified as a critical residue with respect to the Abeta42-lowering response of GSM-1. Finally, we found that GSM-1 responsive and resistant PS mutants behave very similarly towards other potent second-generation compounds of different structural class than GSM-1. Taken together, our data show that a positive Abeta42 response for PS mutants depends both on the particular mutation and the GSM used, and that attenuated Abeta42 responses to low potency GSMs can be overcome for many PS mutants by second generation GSMs.