The first BODIPY library (BD) was synthesized, and a highly selective glucagon sensor, Glucagon Yellow (BD-105), was discovered by fluorescence image-based screening method. BD library was synthesized via a Knoevenagel-type condensation reaction with 160 benzaldehydes and the 1,3 dimethyl-BODIPY scaffold. Using BD compounds, a fluorescence image-based screening was performed against three cell lines including AlphaTC1 and BetaTC6 cells which secret glucagon and insulin, respectively, and HeLa as control cells. Out of the 160 candidate probes, one compound, Glucagon Yellow, exhibited selective staining only in AlphaTC1 cells. The selectivity of Glucagon Yellow toward glucagon was confirmed in vitro by comparison of its fluorescence intensity change against 19 biologically relevant analytes. Subsequent immunostaining experiments revealed that Glucagon Yellow and the glucagon antibody colocalized in pancreas tissue, showing a high quantitative correlation analysis by the Pearson's coefficient constant (Rr ) 0.950). These results demonstrated the potential application of Glucagon Yellow as a glucagon imaging agent in live cells and tissues. © 2009 American Chemical Society.