This collection of readily reproducible Arabidopsis protocols has been updated to reflect recent advances in plant biology, the completion of the Arabidopsis genome sequence, which is essential for studying plant function, and the development of whole systems approaches that allow global analysis of gene expression and protein and metabolite dynamics. The authors have included nearly all techniques developed in Arabidopsis, others recently adapted from the traditional work in crop species, and the most recent ones using Arabidopsis as a model system. Highlights include the most recent methods-transcriptomics, proteomics, and metabolomics - and their novel applications (phosphoproteomics, DNA microarray-based genotyping, high throughput metabolite profiling, and single-cell RNA).