The development of novel transformation vectors is essential to the improvement of plant transformation technologies. Here, we report the construction and testing of a new multifunctional dual binary vector system, pCLEAN, for Agrobacterium-mediated plant transformation. The pCLEAN vectors are based on the widely used pGreen/pSoup system and the pCLEAN-G/pCLEAN-S plasmids are fully compatible with the existing pGreen/pSoup vectors. A single Agrobacterium can harbor (1) pCLEAN-G and pSoup, (2) pGreen and pCLEAN-S, or (3) pCLEAN-G and pCLEAN-S vector combination. pCLEAN vectors have been designed to enable the delivery of multiple transgenes from distinct T-DNAs and/or vector backbone sequences while minimizing the insertion of superfluous DNA sequences into the plant nuclear genome as well as facilitating the production of marker-free plants. pCLEAN vectors contain a minimal T-DNA (102 nucleotides) consisting of direct border repeats surrounding a 52-nucleotide-long multiple cloning site, an optimized left-border sequence, a double left-border sequence, restriction sites outside the borders, and two independent T-DNAs. In addition, selectable and/or reporter genes have been inserted into the vector backbone sequence to allow either the counter-screening of backbone transfer or its exploitation for the production of marker-free plants. The efficiency of the different pCLEAN vectors has been assessed using transient and stable transformation assays in Nicotiana benthamiana and/or Oryza sativa.Plant transformation technologies are fundamental to state-of-the-art plant molecular genetics and crop improvement through genetic engineering (Vain, 2006). Over the past 30 years, the development of novel transformation vectors has been seminal to many breakthroughs in plant transgenesis (for review, see Vain, 2007). In the 1980s, the engineering of Agrobacterium tumefaciens Ti plasmids-namely, the removal of oncogenes and the use of a chimerical gene(s)-led to the production of the first fertile transgenic plants (Zambryski et al., 1983) and the development of binary vectors for plant transformation (Hoekema et al., 1983; Bevan, 1984). Additional types of vectors were developed for direct transfer of DNA into the plant nuclear genome (Paszkowski et al., 1984) and later on into the plastome (Svab et al., 1990). Vector development is particularly important for Agrobacterium-based technologies as binary vectors must comply with, and best exploit, the natural mechanisms and interactions between Agrobacterium and plant cells (Gelvin, 2003). In recent years, the further understanding of T-DNA integration into the plant nuclear genome, combined with an increasing demand for precise and efficient transformation technologies, has created a new opportunity to develop plant transformation vectors with improved characteristics.Since the 1980s, binary vectors for Agrobacteriummediated transformation have been optimized to contain a wide range of selectable marker and reporter genes (Rogers et al., 1987; Becker et al., 1992;Jones et al....