Cotton (Gossypium spp) is an important world crop. Despite the efforts made through traditional breeding methods, cotton breeders still faced with many problems, i.e., narrow genetic base, inability to use alien genes and difficulty in breaking gene linkages. Breeders attempted genetic transformations analyses tools to overcome these problems with very little success, hence the need for transgenic intervention. In this report, an optimized cotton regeneration system from shoot apices used to transform cotton wit insecticidal lectin gene from Allium sativum.Cotton regeneration system was observed to be genotype independent with a regeneration rate of 85% obtained within 16 weeks. The age of explants and the size of isolated tips have a significant effect on shoot tip elongation. The elongation rates of the three varieties were not significantly different from each other (p=0.157 3). It was observed that Samcot 9 had the highest rooting efficiency (47%), and Samcot 13 had the least rooting efficiency (36%). Though the difference in rooting efficiency was not significant in the three varieties (P=0.08). Transgenic cotton plants were obtained via Agrobacterium-mediated transformation using shoot apices as explants. Transformation rate was 1.3% using LBA 4404 with β-glucuronidase (GUS) gene. The mean number of GUS positive apices was 67% higher when acetosyringone was included in the medium. Agrobacterium concentration and co-cultivation time have a significant effect on transient GUS expression. The highest GUS positive number was observed at OD 600 0.6 and co-cultivation for 3 days. Putative transgenic plants were confirmed by leaf GUS assay, kanamycin leaf test and molecular analysis of putative young leaves.