Thermal stability has been proposed as a criterion to assess the allergenic potential of genetically modified foods, but there is a lack of information on relative thermal stability of food allergens vs. nonallergenic proteins. Various methods are commonly used to determine the thermal stability of protein, including the BCA total protein assays, inhibition ELISA assays, Differential Scanning Calorimetry and Far-UV Circular Dichroism Spectroscopy. This study compared the thermal stability of several paired food allergens and nonallergenic proteins by measuring the changes of their solubility, IC50, thermodynamic properties after moist heat. Bovine α-lactalbumin did not exhibit any significant change on solubility after thermal process. Human α-lactalbumin maintained a similar level of solubility during heating, except, after being autoclaved in water, an obvious drop on solubility occurred. Bovine α-lactalbumin revealed small increases on its IgG binding strength after being boiled in water and PBS and autoclaved in water, while autoclaving in PBS led to an opposite trend---a decrease on IgG binding strength occurred. Human α-lactalbumin showed significant increases on its IgG binding strength after moist heat. The solubility of peanut lectin greatly decreased after being boiled or autoclaved in PBS, while boiling or autoclaving in water had little effect on it. Concanavalin A exhibited significant decreases on solubility after being heated in both water and PBS. The IgG binding strength of peanut lectin decreased after being heated in water. An increase for concanavalin A on its IgG binding strength was recognized, during boiling in water and autoclaving in both water and PBS. In summary, bovine α-lactalbumin and peanut lectin are more stable on solubility during autoclaving in water than human α-lactalbumin and concanavalin A. There is no consistent trend on the IgG binding strength change among the paired proteins in our study.