Maize hybrids with improved stover yield and quality are needed to support the emerging cellulosic biofuels industry. Knowledge of the genetic variation, covariation, and genetic architecture of agronomic and cell wall traits will help maize breeders improve relevant traits through selective breeding and genetic engineering. We utilized the maize intermated B73 × Mo17 (IBM) recombinant inbred line (RIL) population to map quantitative trait loci (QTL) and to evaluate the genetic relationships among traits relevant for cellulosic biofuel production, including grain yield, stover yield, neutral detergent fiber digestibility (NDFD), and glucan, xylan, and lignin concentration. Intermated B73 × Mo17 RIL were evaluated per se and as testcrosses to W604S to assess how well performance and QTL effects correspond between inbreds and hybrids. There were no unfavorable correlations between agronomic and cell wall traits within the testcross progeny. Polysaccharide content was either positively correlated to, or not correlated to, NDFD, indicating that increasing both carbohydrate content and convertibility is feasible. Quantitative trait loci were identified for all traits evaluated, but few QTL were in common between inbred per se and testcross evaluations despite moderate to high genotypic correlations between progeny types. This study provides information that will support the development of dual-purpose maize hybrids that are high in grain yield and also high in yield of digestible cellulosic feedstock.