Presenilin (PS)/gamma-secretase degrades transmembrane domains of betaAPP and Notch-1, generating Abeta and NICD. Some cleavages by PS/gamma-secretase have diversity. gamma-Cleavage of betaAPP occurs mainly at residue 40 (gamma40) and at residue 42 (gamma42), producing Abeta 40 and Abeta42, respectively. An increase in the proportion of gamma42 to gamma40 cleavage is consistently observed in many familial Alzheimer disease-associated PS or betaAPP mutants, but it is unclear whether such changes in the precision of PS/gamma-secretase have any biological effects. We found that S3 cleavage of Notch-1 by PS/gamma-secretase has diversity, resulting in the production of two types of NICD with distinct ability to transmit Notch signaling. We also showed that the precision of S3 cleavage and Notch signaling intensity can be modulated by physiological factors. Although some PS/gamma-secretase modulators (GSM) have been known to change the precision of gamma-cleavage, it is unknown whether there are any modulators which change the S3 cleavage precision. We found such a compound increasing Notch signaling intensity. Our findings suggest that i) abnormally up-or-down regulated Notch signaling may be corrected by modifying the S3 cleavage precision and that ii) effects on the S3 cleavage precision should be carefully examined in developments of GSM lowering Abeta42 for AD therapeutics.