Qualitative and quantitative PCR assays were developed for detection of commercialised Bt cotton events, i.e. MON531, MON15985 and other Bt crops, which are under different stages of field trials in India, i.e. Bt brinjal, Bt rice, Bt cauliflower, Bt potato and Bt okra. Multiplex PCR assays simultaneously detecting specific cry1Ac, cry1Ab, cry2Ab genes, Cauliflower Mosaic Virus 35S promoter, nptII marker gene along with species- or taxon-specific endogenous gene in these Bt crops have been developed. The quantitative real-time PCR assays were also reported for cry1Ac gene using designed primers and TaqMan probe. The sensitivity of developed assays for detection of specific transgene was established up to 0.01%. The analytical methods developed in the present report will be of immense use for qualitative screening and detection of Bt crops along with the quantitative analysis of inserted cry1Ac gene to meet the threshold level for regulatory compliance.