Studies on the comparative performance of Bollgard and Bollgard II Bt cotton genotypes against insect pest scenario, Cry protein expression levels was undertaken at College of Agriculture and RARS, Raichur, Karnataka during 2008-09. Bt cotton genotypes (BG-I, BG-II) under protected condition responded similarly for sucking pests viz., thrips, leafhoppers, aphids, whiteflies, mirid bug, mealy bug, red cotton bug and dusky cotton bug. There was no variation in the egg population of H. armigera among the different genotypes. With respect to larval incidence and damage due to H. armigera, E. vittella, S. litura and P. gossypiella, all the BG-II genotypes performed better over BG-I genotypes under unprotected condition. There was no significant difference with respect to natural enemies (grub and adults of coccinellids, Chrysoperla carnea, spiders and anthocorids) among the Bt cotton genotypes (BG-II, BG-I). Cry protein levels were high in leaves followed by squares and boll rind at early stages of crop growth (100 DAS) which went on decreasing and reached minimum at 160 DAS.