Abstract Individuals are genetically variable for the way in which they process nutrients and in the effects of dietary content on reproductive success, immunity, and development. Here, we surveyed genetic variation for nutrient stores (glucose, glycogen, glycerol, protein, triglycerides, and wet weight) in the Drosophila Genetic Reference Panel (DGRP) after rearing the flies on either a low-glucose or high-glucose diet. We found significant genetic variation for these nutritional phenotypes and identified candidate genes that underlie that variation using genome-wide associations. In addition, we found several significant correlations between the nutritional phenotypes measured in this study and other previously published phenotypes, such as starvation stress resistance, oxidative stress sensitivity, and endoplasmic reticulum stress, which reinforce the notion that these lines can be used to robustly measure related phenotypes across distinct laboratories.