Much of our modern maize germplasm was originally brought about by the combination of northern flint lines and southern dent lines. Yet commercial production in the US today is dominated by dent or semi-dent kernel type maize (Corn Belt dent), which has hard outer walls of endosperm surrounding a soft floury interior that when dried compacts to form the characteristic dent in the top of the kernel. One major exception is flint type corn, which is grown in areas of North America, Europe, South America, the Caribbean and many parts of Africa. Flint maize is characterized by its rounded vitreous outer endosperm and soft granular center and has desirable qualities such as cold tolerance, disease and insect resistance as well as longer storage capacity than many dent lines. The Nested Association Mapping (NAM) population parent inbred lines represent many of the major kernel types found in maize. In 2006 the entire NAM population of recombinant inbred lines were grown and scored visually for kernel type, in five locations. The NAM population contains 25 parents, of which, there are nine flint, nine semi-dent, four dent, two sweet and one popcorn parent lines, with a common dent parent, B73. Linkage mapping with ~7400 intervals markers was used to examine the genetics of kernel morphology. This yielded several areas of the genome that are significantly associated with the difference in kernel type seen in NAM. Several other major and minor QTL are shared across many families. Genome wide association study (GWAS) was also used in the maize association panel. Suggested peaks from both linkage mapping and GWAS highlight 13 candidate genes in starch and protein related pathways in the endosperm.