The ipt gene was used in the ipt-type MAT vector system as a positive selection for transformed cells. This system is visual selection of morphological changes of transformed shoots induced by increase endogenous cytokinin. This system is also involved elimination of the ipt gene that is mediated by the sitespecific recombination system by R/RS derived from Zygosaccharomyces rouxii resulting in marker-free transgenic plant (MFTP). The cotyledon explants of tomato (Lycopersicon esculentum Mill.) cv. VF-13 4 -12 were transformed by Agrobacterium tumefaciens strain AGL-1 harboring pMAT21 or pEXM2 vector. The optimum conditions for ipt-shooty production were the use of Agrobacterium culture with OD 600 = 0.60.8 diluted to 1:10 and with final OD600 = 0.25 dilution for pMAT21 and pEXM2 vectors, respectively. In addition, the optimum time for incubation of cotyledon explants and bacterial cultures was 30 min for both pMAT21 and pEXM2 vectors. Under the optimum conditions for transformation in this study, the percent age of bud regeneration per total explants was 52% and 48%, and development to ipt-shooties were 19% and 11% for pMAT21 and pEXM2 vectors, respectively. In PCR analysis, 100% of ipt-shooty lines transformed with both vectors were ipt-positive. However, only phenotypically normal shoots derived from transformation with pMAT21 using bacterial culture with final OD600 0.25 and 30 min-incubation were marker- free transgenic tomatoes.