Abstract Cotyledons excised from seedlings of Cajanus cajan (pigeonpea) were grown on media containing cytokinins (6-benzyladenine, zeatin, and zeatin riboside) and an allied compound, thidiazuron. With the exception of zeatin riboside, initial response in terms of induction of organized structures was very high. However, subsequent regeneration of shoots from cotyledon explants was very poor. Anatomical studies on the regenerating explants were undertaken to study the pattern of morphogenesis. Cytokinins and thidiazuron induced divisions in the epidermal and sub-epidermal cell layers leading to the formation of primary protrusions on the surface. This was followed by the development of foci of high meristematic activity either on the surface or within the primary protrusions. These foci differentiated into embryo-like structures or shoot meristem-like structures. Mostly aberrant shoots, with poorly developed apical meristems, regenerated from these structures.