Soybeans in general contain 35-40% protein. Efforts are underway to increase further this protein content, thus enhancing their nutritive value. Even though higher protein is a desirable characteristic, whether such an increase will be accompanied by enhanced protein quality is not known. Soybean protein quality could be significantly improved by increasing the concentration of the sulfur-containing amino acids, cysteine and methionine. To ascertain if a correlation existed between protein quantity and quality, a comparison of the amino acids of soybeans differing in protein content was made. Soybeans with higher protein content had a significantly lower percentage of sulfur amino acids, while those with lower protein exhibited a higher content of cysteine and methionine. Nitrogen application elevated the protein content but lowered that of the sulfur amino acids. Transmission electron microscopy examination of thin sections of low protein soybean seeds revealed several protein storage vacuoles that were partially filled with storage proteins. Fluorescence two-dimensional difference gel electrophoresis of soybean seed proteins revealed that nitrogen application favored the accumulation of the beta-subunit of beta-conglycinin while decreasing the accumulation of Bowman-Birk protease inhibitor (BBI), a protein rich in cysteine. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of 60% 2-propanol-extracted proteins showed a drastic reduction in the accumulation of BBI with increasing protein content. Northern blot analysis indicated that nitrogen had a negative influence on the expression of the BBI gene. Our results indicate that the negative correlation between total protein and sulfur amino acid content is mostly mediated by the differential accumulation of BBI.