The maize kernel plays a critical role in feeding humans and livestock around the world and in a wide array of industrial applications.  An understanding of the regulation of kernel starch, protein, and oil is needed in order to manipulate composition to meet future needs.  We conducted joint linkage quantitative trait locus (QTL) mapping and genome-wide association studies (GWAS) for kernel starch, protein, and oil in the maize nested association mapping (NAM) population.  Joint linkage mapping revealed that kernel composition traits are controlled by 21 to 26 QTL.  GWAS was conducted using 1.6 million markers from the maize HapMap project.  Numerous GWAS associations were detected including several oil and starch associations in DGAT1-2, a gene which regulates oil composition and quantity.  Results from NAM were verified in a 282 diverse inbred association panel using both GWAS and candidate gene association approaches.  We identified many beneficial alleles that will be useful for improving kernel starch, protein, and oil content. By stacking the most favorable alleles from each parent into B73, we can improve the starch content of B73 by 10% and oil content by 3.6%.