The current research work was undertaken to characterize different Pakistani wheat varieties for physicochemical, rheological, technological and immunochemical characteristics. The modification of wheat gluten through methionine binding to develop bread for celiac disease patients was also the main aim of this study. The results revealed that wheat varieties differ significantly for the characteristics studied. Significant effect of crop year was observed on grain width, moisture content, falling number value and dough rheological parameters. The antibody response against glutenin and HMW-GS was positively correlated to the total score of breads, chapattis and naans. The electrophoretic patterns of molecular weight of glutenin subunits of different wheat varieties showed the presence of glutenin subunits in the range of 28.23 to 110.89 kDa and 28.29 to 113.51 kDa, while total gliadin electrophoregrams ranged from 31.03 to 89.61 kDa and 32.91 to 92.22 kDa among different wheat varieties during the crop years 2010-11 and 2011-12, respectively. The wheat variety AARI-11 outperformed other varieties in most of the physico-chemical, rheological and technological characteristics. Therefore, it was selected for gluten modification. The immunoreactivity to the modified gluten proteins was decreased as the reaction proceeds and minimum immunoreactivity (26±0.37%) was observed near to 60 minutes of reaction time with 5% methionine added to the system. The results showed that the serum of each patient had positive IgA index to gliadins from unmodified gluten, but just sera of two patients had positive IgA index to gliadins from modified gluten and when these proteins were digested the sera of no patient’s serum had positive IgA reactivity. The gluten content in breads prepared with modified gluten was observed to be 79 ppm, which is within the limits set by Codex Alimentarius Commission. The study concludes that the methionine binding to gluten induced a remarkable reduction of celiac IgA immunoreactivity to gliadin. ELISA is a reliable method and can be used as single tool for the wheat quality assessment therefore it should be developed for all wheat varieties. Prospectus of modified gluten for different wheat based foodstuffs like the assayed bread in this study needs to be investigated. A research project should also be conducted to investigate the antibody response of modified gluten.