Cytokinins 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.