Biochemical studies were carried out on Laxmi, Abhadita, DCH-32 and RCH-2 Bt, JKCH-1 Bt, JKCH-2 Bt, of non-Bt and Bt genotypes of cotton , respectively. All the test genotypes were found susceptible to the Alternaira blight disease. The results indicate that non-Bt genotypes recorded high amount of total protein (7.19 to 9.18%) as compared to Bt genotypes, but total phenol ( -17.79 to -18.39 % ), total sugar (-12.17 to -12.82 %) and reducing sugar (-4.51 to -19.05%) recorded lower amount compared to Bt genotypes. Further, the decrease in total protein (-18.43 to -19.85%), total phenol (-32.76 to -38.63), total sugar (-31.00 to -33.36%) and reducing sugar (-27.99 to -40.86) was more in infected plants of Alternaria blight disease.