Seed cell wall polysaccharides (CWPs) represent a significant portion of seed dry matter (DM) in soybean [Glycine max (L.) Merr.]. Quantitative trait locus (QTL) analysis is a step toward identifying genes controlling CWP concentration and composition of soybean seed. The objectives of this study were to identify QTLs associated with CWP variability and investigate the relationships between seed CWP, protein, and oil content. Whole soybean seed from 'Minsoy', 'Archer', and 108 Minsoy X Archer recombinant inbred (RI) lines were analyzed for CWP using the Uppsala total dietary fiber method. For a random subsample of 73 RI lines, embryos (seed with the seed coats removed) were analyzed. Three QTLs were observed on Linkage Groups U3 (ISU A2), U7 (ISU A1), and U24 (ISU K) that represented most of the variability in CWP content expressed on a DM basis in both whole seed and embryos. A QTL for fucose was detected on U3. Linkage Group U7 contained multiple QTLs mapping at the same location for galactose, the arabinose-to-galactose ratio (Ara/ Gal), pectin, and CWP content. A QTL for arabinose was on U24. These same chromosomal regions also exhibited significant QTLs when the monosaccharide data were expressed on a CWP basis, suggesting that most of the variation in CWP was controlled by changes in the incorporation of galactose, arabinose, and fucose into CWP as total CWP concentration increased. Negative correlations of protein with oil, and the sum of protein and oil with most monosaccharides, pectin, and CWP were present within the RI population, indicating that decreasing seed CWP content will improve seed quality.