The direct protein-protein interaction between the phosphatase calcineurin and transcription factor NFAT plays important roles in a number of crucial mammalian cell signaling and regulatory events, such as activation of T cells and developmental genetic programs. In this paper, we report on the identification of small organic molecules for the targeted disruption of the NFAT-calcineurin interaction in vitro. In the preceding paper (21), we devise a theoretical and procedural framework for high-throughput fluorescence polarization screens to aid in this effort. The results presented here ground on this work and illustrate the stringency and successful general applicability of our approach. The identified compounds provide valuable molecular tools for probing calcineurin signaling and for the NFAT-specific inhibition of calcineurin in cells and organisms.