The availability of complete plant genome sequences has opened a new era of plant molecular research using approaches such as comprehensive expression analysis, ectopic expression and gene knockdown. For Such purposes, new tools realizing easy and rapid construction of recombinant plasmids are required. Here, we describe Gateway cloning compatible binary vectors for post-genomic research in plant genetic engineering. The vectors comprise a variety of reporters, epitope tags and selective markers that should make them useful for construction of plasmids for Agrobacterium-mediated transformation of plants. We also describe vectors for promoter swapping using Gateway cloning technology.