The recent explosion in available genome sequence data has ushered in an era in which analysis of a whole genome can be performed in a single experiment. While DNA microarrays have long been the established technology for measuring gene expression levels, standard expression arrays use relatively few probes for each gene and are typically biased toward known and predicted gene structures. Recently, with the availability of complete genome sequences for many organisms, very-high-density oligonucleotide-based microarrays that span the entire genome have emerged as the preferred platform for genomic analysis. Whole-genome tiling microarrays can be employed for a myriad of purposes, including empirical annotation of the transcriptome, chromatin immunoprecipitation-chip studies, analysis of alternative RNA splicing, characterization of the methylation state of cytosine bases throughout a genome (methylome), and DNA polymorphism discovery. Here, we review several applications of whole-genome technology to obtain a variety of genomic-scale information in plants.