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Fitness costs associated with resistance to Bacillus thuringiensis (Bt) crops are expected to delay the evolution of resistance. In a previous study where pink bollworm, Pectinophora gossypiella (Lepidoptera: Gelechiidae), larvae overwintered in outdoor insectaries, individuals from Bt-resistant strains had lower survival than individuals from Bt-susceptible strains or F1 progeny from crosses between resistant and susceptible adults. To investigate the physiological basis of such recessive cost, diapause duration was experimentally manipulated in the laboratory. Compared to a Bt-susceptible strain and F1 progeny, we hypothesized that Bt-resistant strains could exhibit a lower propensity or intensity of diapause, faster weight loss during overwintering, lower initial weight of diapausing larvae, and reduced longevity of moths emerging from diapause. Results were as expected for initial weight of diapausing larvae and longevity of overwintered male moths or female moths remaining in diapause for a short period. However, a higher diapause induction and intensity and slower weight loss occurred in F1 progeny and Bt-resistant strains than in a Bt-susceptible strain. Moreover, F1 progeny had greater overwintering survival than the Bt-resistant and Bt-susceptible strains, and F1 female moths had the greatest longevity after sustaining long diapausing periods. All of these unexpected results may be explained by pleiotropic effects of resistance to Bt cotton that increased the strength of diapause in the F1 progeny and Bt-resistant strains. Incomplete resistance was reflected in disadvantages suffered by Bt-resistant individuals feeding on a Bt diet instead of a non-Bt diet, including lower diapause propensity, lower diapause intensity and reduced longevity of overwintered male moths. While this study suggests that the evolution of resistance to Bt cotton and feeding on a Bt diet in Bt-resistant individuals have pervasive effects on several traits associated with diapause, further field experiments are needed to elucidate the basis of the overwintering cost in the pink bollworm.