A new aspect of protein immunogenic and allergenic properties has become important recently, when there is a higher chance that our immune system will be exposed to novel protein antigens and/or familiar protein antigens with an unprecedented high frequency and large amount. These proteins are innocuous, nontoxic, and noninvasive by themselves, and include various natural proteins from the environment and recombinant proteins from industry. The technical term allergenic has been used for such proteins and their abilities to induce specific IgE production and to cross-link IgE/Fc epsilon RI on the surface of mast cells and basophiles have been recognized. As for the environmental proteins, some physicochemical properties (solubility, stability, and permeability across a mucosal epithelium) of the proteins indirectly play important roles in their allergenic potential because they do not originate from invasive pathogens as vehicles. Indeed, several lines of experimental evidences have been accumulated indicating that all proteins are absorbed across mucosal epithelia by transcellular transport and/or through interstitial spaces among the epithelial cells but not at equal levels. Some animal models have been established for natural sensitization to some allergenic proteins by feeding or intragastric administration without an adjuvant and, in a few cases, some symptoms resembling human allergy and even anaphylaxis have been induced by oral challenge with the proteins. Sometimes, even to self-proteins, the immunogenic or allergenic potential is given by post-translational modifications and possibly by unknown structural/conformational alterations, when they are exogenous self-proteins, such as recombinant human proteins for drug use. Despite the accumulation of knowledge and the progress in analytical technology on protein allergenicity, it is still crucial to predict the allergenic potential of novel and unused proteins. However, some animal models are applicable for assessing the relative allergenic potential of processed proteins in comparison with that of native proteins in preclinical studies.