SummaryCytokinins are hormones that regulate many developmental and physiological processes in plants. Recent work has revealed that the cytokinin signal is transduced by two‐component systems to the nucleus where target genes are activated. Most of the rapid transcriptional responses are unknown. We measured immediate‐early and delayed cytokinin responses through genome‐wide expression profiling with the Affymetrix ATH1 full genome array (Affymetrix Inc., Santa Clara, CA, USA). Fifteen minutes after cytokinin treatment of 5‐day‐old Arabidopsis seedlings, 71 genes were upregulated and 11 genes were downregulated. Immediate‐early cytokinin response genes include a high portion of transcriptional regulators, among them six transcription factors that had previously not been linked to cytokinin. Five plastid transcripts were rapidly regulated as well, indicating a rapid transfer of the signal to plastids or direct perception of the cytokinin signal by plastids. After 2 h of cytokinin treatment genes coding for transcriptional regulators, signaling proteins, developmental and hormonal regulators, primary and secondary metabolism, energy generation and stress reactions were over‐represented. A significant number of the responding genes are known to regulate light (PHYA, PSK1, CIP8, PAT1, APRR), auxin (Aux/IAA), ethylene (ETR2, EIN3, ERFs/EREBPs), gibberellin (GAI, RGA1, GA20 oxidase), nitrate (NTR2, NIA) and sugar (STP1, SUS1) dependent processes, indicating intense crosstalk with environmental cues, other hormones and metabolites. Analysis of cytokinin‐deficient 35S:AtCKX1 transgenic seedlings has revealed additional, long‐lasting cytokinin‐sensitive changes of transcript abundance. Comparative overlay‐analysis with the software tool mapman identified previously unknown cytokinin‐sensitive metabolic genes, for example in the metabolism of trehalose‐6‐phosphate. Taken together, we present a genome‐wide view of changes in cytokinin‐responsive transcript abundance of genes that might be functionally relevant for the many biological processes that are governed by cytokinins.