We performed a genome-wide association study and identified several genes involved in the genetic control of the natural variation for tocochromanols (vitamin E and antioxidants), carotenoids (provitamin A, lutein, zeaxanthin), and minerals in fresh sweet corn kernels (~21 DAP). For tocotrienols, we also identified associations with two starch biosynthetic genes (su1 and sh2) specific of sweet corn, and reported evidence for the involvement of sh2. Whole-genome prediction models had moderate prediction abilities for most of the phenotypes measured in the three studies, indicating that these models may be used for developing sweet corn lines with nutrient-dense kernels. Together, these studies represent the most extensive assessment of natural variation for vitamins and minerals in fresh sweet corn kernels and constitute a key step for improving the nutritional quality of sweet corn for human health.