A global analysis of gene expression events during shoot development in Arabidopsis was conducted using oligonucleotide array analysis. Shoots can be induced in tissue culture by preincubating root explants on an auxin-rich callus induction medium (CIM) and by transferring explants to a cytokinin-rich shoot induction medium (SIM), during which time explants become committed to shoot formation and ultimately form shoots. Oligonucleotide array data obtained during shoot development from approximately 8000 Arabidopsis genes were subjected to principal component analysis, which demonstrated that the major components of variation in gene expression during shoot development can be represented by groups of genes, each group of which is upregulated at only one developmental stage. Two percent to three percent of the approximately 8000 Arabidopsis genes monitored in this study were upregulated by fourfold or more at any one stage during shoot development. When upregulated and downregulated genes were categorized by function, it was observed that numerous hormone response genes were upregulated during preincubation on CIM. Groups of genes involved in signaling and/or transcription were induced at or before the time of shoot commitment, and genes that encode components of the photosynthetic apparatus were upregulated later in development before shoot emergence. Primary hormone response genes, such as Aux/IAA genes, were upregulated during preincubation on auxin-rich CIM, and cytokinin-responsive response regulator genes were upregulated during incubation on cytokinin-rich SIM. The expression of ARABIDOPSIS RESPONSE REGULATOR5, a type-A response regulator gene, was upregulated at the time of shoot commitment, and its expression was localized to sites of presumptive shoot formation. Two "hybrid" His kinases involved in cytokinin responses, CRE1, which encodes a cytokinin receptor, and CKI1, a gene that is capable of conferring cytokinin-independent shoot development, were upregulated during incubation on SIM.