A protocol is presented for rapid genotype-independent transformation and regeneration of cotton (Gossypium spp.) from shoots isolated from germinating seedlings. Isolated shoots are inoculated with a super-virulent strain of Agrobacterium tumefaciens, subjected to a mild antibiotic selection, and directly regenerated as shoots in vitro. Shoots do not dedifferentiate and mutation rates are low. Rooted shoots can be obtained within 6–10 weeks of isolation and inoculation depending on the cotton cultivar.