Soybeans contain isoflavones which have been associated with antioxidative and anticancer activity. Oil, protein and amino acid content are seed quality measures important in processing and use. The objective of this study was to evaluate effects of different scion and rootstock combinations on levels of isoflavone, oil, protein and amino acids in soybean seed. Three soybean varieties (USG 5601T, PI416.937, Williams 82)which differ significantly in isoflavone, oil, and protein levels as well as root and canopy morphology were chosen. USG 5601T has normal tap roots and leaflets which orient strongly with sunlight. Williams 82 has normal roots and leaflets which orient moderately. PI416.937 has prolific rooting and leaflets which orient minimally. Non-grafted plants, self grafts and reciprocal grafts of scions and rootstocks were prepared among the three varieties. The 12 treatment combinations were grown in the field at Knoxville, TN (latitude 35°49¢ N, longitude 83°58¢ W) in an RCB design with six replications in 2003 and three replications in 2004. soflavone, oil, protein, and amino acid levels were measured using HPLC and NIR methods. Grafting did not significantly affect levels of isoflavone, oil, or protein in the treatments. Scions had significant effects on isoflavone, oil, protein, and amino acid levels; however this was not true for rootstocks. No significant interactions were detected among scion/rootstock combinations for effects on isoflavone, oil, protein, or amino acid levels. Negative correlations were detected between oil and isoflavone (r = -0.608, p<0.001) and between protein and oil concentrations (r = -0.599, p<0.001). No significant correlation was detected between protein and isoflavone content (r = -0.045, p = 0.704). The above ground portion of the soybean plant appears to be the dominant factor determining levels of isoflavone, oil, protein, and amino acids in seed. Rootstocks had no significant (p<0.05) effects on the measured seed constituents.