Agrobacterium-mediated transformation is the most common method for the incorporation of foreign genes into the genome of tomato as well as many other species in the Solanaceae family. This chapter describes a protocol for the genetic transformation of tomato cultivar Micro-Tom using cotyledons as explants. Detailed procedures are also included for determining gene-copy number using a duplex qPCR TaqMan assay, and the histochemical analysis of GUS expression.