Helicoverpa armigera (Hubner) populations collected from different cotton-growing areas of Punjab and Rajasthan (India) were studied for change in the baseline susceptibility (LC50) to Cry1Ac and impact of continuous laboratory selection of this pest on Cry1Ac toxin protein. Two years of Bt-cotton cultivation in these states did not result in any significant changes in susceptibility of H. armigera with LC50 values (microg Cry1Ac/ml of SS (semi-synthetic) diet) for populations from this cotton-growing area ranging between 0.109 to 0.203 in 2005 compared to 0.140 to 0.223 in 2006. As this was indicative of a low change in tolerance levels, the susceptibility differences observed among different populations were attributed to existence of genetic variability/molecular differences, which were established using comparative RAPD profiles. On an average, the tolerance levels of these populations to Cry1Ac-showed only 1.57 to 2.91 fold increase in 2005 and 2.02 to 3.23 fold in 2006, compared to the values of a susceptible population established in 2002 i.e., three years before the approval of Bt cotton cultivation in these two states. The laboratory selection (0.1 microg Cry 1Ac/ml diet) of these populations for six continuous generations resulted in decrease in susceptibility with LC50 values ranging from 0.165 to 0.311 microg/ml diet for seven populations from Punjab and Rajasthan. However, this improvement in tolerance level of H. armigera was associated with increased larval mortality, decreased pupation and adult emergence, low rate of fecundity and decreased hatching of eggs coupled with numerous deformities as compared to populations on normal diet. This higher level of fitness cost that was observed during selection of earlier generation of H. armigera however showed a continuous decline as the populations entered into subsequent generation thus resulting in improved survival due to decrease in per cent deformities of different development stages. The observed high fitness cost of H. armigera even at Cry1Ac level is much lower than the expressed toxin levels in most Bt-cotton hybrids goes against the possibility of a rapid resistance development in this pest.