Knowing when and where a given protein is activated within intact animals assists in elucidating its in vivo function. With the use of a genetically encoded A-probe (activation bioprobe), we revealed that Cdc42 guanosine triphosphatase (GTPase) remains inactive within Drosophila embryos during the first two-thirds of embryogenesis. Within the central nervous system where Cdc42 activity first becomes up-regulated, individual neurons display patterns restricted to specific subcellular compartments. At both organismal and cellular levels, Cdc42's endogenous activation patterns in the wild type allow predictions of where loss-of-function phenotypes will emerge in cdc42/cdc42 mutants. Genetic tests support the importance of suppressing endogenous Cdc42 activities until needed. Thus, bioprobe-assisted analysis uncovers how ubiquitously expressed signaling proteins control cellular events through continual regulation of their activities within animals.