Yellow pea flour contains very low quantity of prolamins, thus it could be a good alternative dietary source for individuals suffering from celiac disease or wheat allergy. Beside emulsifiers, enzymes can be used for developing noodle structure with high quality. Transglutaminase (TG) enzyme was tested in model systems for improving noodle structure by using beneficial cross-linking property of the enzyme. Sensory-and cooking properties and biochemical attributes of proteins were evaluated to characterize structure-function relationships in accordance with the concentration of the applied enzyme. The amount of water and salt soluble protein fractions was reduced meaningfully and the molecular weight distributions assessed by SDS PAGE were changed by addition of 50–200 mg kg
TG enzyme. At the same time, sensory properties were improved and high water uptake and low cooking loss were also observed. Forasmuch an increase has been expected in the amount of the cross-linked molecules, the cross-reactivity of prolamins with anti-gliadin antibody was also tested to reduce the risk related to gluten sensitivity. Finally, the possible contamination with wheat was controlled by DNA-based PCR.