For many years, the plant hormones auxin, cytokinin, ethylene, gibberellin, abscisic acid, brassinosteroid, jasmonic acid, and salicylic acid have been extensively studied as key regulators of plant growth and development. However, recent biochemical and genetic analyses have revealed that secretory peptides are also responsible for intercellular signaling in plants and regulate various events including wound response, cell division control, and pollen self-incompatibility. We discovered two natural CLAVATA3 (CLV3)/ESR-related (CLE) peptides: tracheary elements differentiation inhibitory factor (TDIF) and CLV3, which are dodecapeptides with two hydroxyproline residues that regulate vascular development and meristem formation, respectively. This discovery enabled us to predict the chemical form of CLE gene products. In the Arabidopsis genome, there are 31 CLE genes that correspond to 26 CLE peptides. The application of all 26 chemically synthesized peptides to plants revealed the existence of distinctive functional groups. From these results, we discuss the functions of CLE peptides in plant development and plant-parasite interactions.