Genomic programs are yielding tremendous amounts of data about plant genomes and their expression. In order to exploit and understand this data it will be necessary to determine the mechanisms leading to natural variation of patterns of gene expression. The ability to understand how gene expression varies among populations (and not only within the population used in the genomics program) and following the exposure of plants to various stress conditions will be fundamental to progress in the post-genomics phase. Transposable elements (TEs) make up nearly half of the total amount of DNA in many plant genomes, so definition of their influence on genome structure and gene expression is of clear significance to the understanding of global genome regulation and phenotype variations. We describe here the different types of plant TEs and recent examples on how they contribute to structure, evolution and genetic control architecture of plant genomes.