The role of intercellular signals in plant development was investigated using phytochrome-induced formation of anthocyanin in cotyledons of white mustard as a model system. The problem was approached by irradiating different subregions of the cotyledon with a microbeam. This technique was combined with in situ hybridization of chalcone synthase mRNA after irradiation of the entire cotyledon. Individual cells that exhibited all-or-none responses with a resultant stochastic, patchy pattern were examined during early stages of anthocyanin synthesis. It was demonstrated that the responses of individual cells were subsequently integrated by long-range inhibitory signals. This process led to ordered and gradually developing patterns that could be detected when final stages were analyzed at the whole-organ level. The significance of these findings is discussed in terms of efforts toward a general understanding of photomorphogenesis in plants.