The effect of germination and subsequent heat-processing on the degradation of soluble proteins, including some allergenic proteins, in brown rice grains was investigated. The content of soluble proteins, including 14-16-kDa and 26-kDa allergens, in the germinated and processed brown rice grains (GPR) was much lower than that of non-germinated brown rice. These proteins in brown rice grains were also much lower after subsequent heat-processing during the manufacturing process. The protease activity of germinated brown rice (GR) was detected and increased 1.5 times after germination. The optimum pH values for degradation of the 26-kDa and 14-16-kDa allergens in the GR grains were 4 and between 5 and 7, respectively. These results suggest that the decrease in the soluble proteins and allergens was induced in part by proteolytic degradation. The presence of a detergent enhanced the proteolytic degradation of the soluble proteins, especially of the 26-kDa allergen, in the brown rice grains. The degradation of the 26-kDa allergen was weakly inhibited by NEM, suggesting cysteine protease(s) may have been involved in its degradation. These results suggest that the two abundant allergens were degraded in a different manner and probably by different proteases in the grains during germination.