Transglutaminase (TG) enzyme was tested in T. aestivum and T. durum wheat-based model systems to evaluate the quality improvement to pasta imparted by cross-linking. Quality was measured by the enhancement in sensory and cooking properties. In this process, tests were also performed to establish the biochemical structure-functions of the proteins involved at TG enzyme concentrations between 10 and 200 mg kg−1. It was observed that the amounts of water/salt-, the alcohol- and the alkali-soluble protein fractions were reduced significantly. Change in the molecular weight distribution assessed by SDS PAGE was also noticed. The sensory properties were observed to improve from high water uptake and low cooking loss. The TG treatment changed the gluten structure in the modified pasta products. Immune-reactive gliadin fractions were detected by immunoblotting and independently measured by competitive indirect ELISA, using the anti-gliadin rabbit IgG.