Production of transgenic cotton from Agrobacterium tumefaciens strain LBA4404 harboring the recombinant binary vector pBI121 containing the chi gene (pBI121-chi) and neomycin phosphotransferase (nptII) gene has been used. In order to confirm transgenic cotton, molecular analysis methods are used. Polymerase chain reaction (PCR) and Southern blot analysis are used to confirm the integration transgenes into the plant genome. Western immunoblot analysis of proteins are extracted from leaves of transgenic cotton, which reveals the presence of an immunoreactive band with MW of approximately 31 kDa in transgenic cotton lines using anti-chitinase-I polyclonal anti-serum. Although there are other molecular methods, PCR, Southern blot, and Western blot are the most important of them, which will be discussed in this chapter.