Seeds from three soybean genotypes were tested to evaluate the effect of fungal damage by Fusarium spp and Diaporthe/Phomopsis complex on protein quantity and quality. Fungus-infected seeds had higher protein contents than uninfected ones. A selective degradation of soluble proteins was detected in seeds infected with either fungus. Some of the storage proteins degraded were identified as α , α and β subfractions of the β-conglycinin, and A 3 subfraction of the glycinin. Furthermore, reductions in lipoxygenase and trypsin inhibitor activities were observed in fungus-infected seeds. Amino acid composition did not vary between infected and uninfected seed lots, so protein degradation should not affect amino acid structures.