Mutual interactions of the phytohormones, cytokinins and auxin determine root or shoot identity during postembryonic organogenesis in plants. However, our understanding of the role of hormonal metabolism and perception during early stages of cell fate reprogramming is still elusive. Here we show that auxin activates root formation, whereas cytokinins mediate early loss of the root identity, primordia disorganisation and initiation of shoot development. Exogenous and endogenous cytokinins influence the initiation of newly formed organs, as well as the pace of organ development. The process of shoot apical meristem establishment is accompanied by accumulation of endogenous cytokinins, differential regulation of genes for individual cytokinin receptors, strong activation of AHK4-mediated signalling and induction of the shoot-specific homeodomain regulator The last is associated with upregulation of isopentenyladenine-type cytokinins, revealing higher shoot-forming potential when compared with-zeatin. Moreover, AHK4-controlled cytokinin signalling negatively regulates the root stem cell organiser in the root quiescent centre. We propose an important role for endogenous cytokinin biosynthesis and AHK4-mediated cytokinin signalling in the control of-induced organ identity.