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In this study transgenic plants of sour orange (C. aurantium) that is an important citrus rootstock were produced by Agrobacterium-mediated transformation. Epicotyl and hypocotyl segments-derived explants were co-cultured with Agrobacterium strain EHA105 carrying pFGC5941 plasmid containsing CTV coat protein (p25) gene. One of the main objects of present research was to improve the direct in vitro organogenesis efficiency in C. aurantium. Therefore different combination of BAP (0, 1, 2 mg/L) and NAA (0, 0.25, 0.5 mg/L) were used in selective medium to culture transformed explants. The highest regeneration (57%) was obtained from explant treated with 2 mg/L BAP and 0.25 mg/L NAA. Effects of wounding and vacuum infiltration on transformation efficiency were evaluated either. The best transformation efficiency (11.25%) was obtained from explants that were vacuum infiltrated during transformation and subsequently were cultured in medium containing 2 mg/L BAP and 0.25 mg/L NAA. PCR analysis using two different genes were performed to confirm transformation. Micro grafting of transformed shoots were carried out on non-transgenic, in-vitro grown seedlings.