ABSTRACT A biophysical survey was conducted in 15 cotton-growing districts of Pakistan. Four hundred cotton growers were approached and inquired about the production technology of Bt cotton. Further, 25 strip tests using combo strips (Cry1Ac, Cry2Ab, Vip3Aa and Cp4, EPSPS gene) were performed at each farmer’s field. Out of 10,000 total-tested samples, farmers claimed 9682 samples as Bt and 318 samples as non-Bt. After performing a strip test, 1009 and 87 samples were found false negative and false positive, respectively. Only 53 samples were found positive for Cry2Ab, 214 for EPSPS and none for Vip3Aa gene. Quantification of Cry endotoxin and bioassay studies were performed by taking leaves from upper, middle, and lower canopies, and fruiting parts at approximately 80 days after sowing from 89 varieties. Expression was highly variable among different canopies and fruiting parts. Moreover, Cry endotoxin expression and insect mortality varied significantly among varieties from 0.26 µg g−1 to 3.54 µg g−1 with mortality ranging from 28 to 97%, respectively. Highest Cry1Ac expression (3.54 µg g−1) and insect mortality (97%) were observed for variety FH-142 from DG Khan. Cry endotoxin expression varied significantly across various plant parts, i.e., IUB-13 variety from upper canopy documented 0.34 µg g−1 expression with 37% insect mortality in Layyah to 3.42 µg g−1 expression and 96% insect mortality from DG Khan. Lethal dose, LD95 (2.20 µg g−1) of Cry1Ac endotoxin was optimized for effective control of H. armigera. Our results provided evidence of practical resistance in H. armigera and way forward.