To determine the extent to which sulfur (S) and nitrogen (N) fertility interact to influence the flavor biosynthetic pathway in onion (Allium cepa L.), `Granex 33' onions were grown in hydroponic solution culture with varying levels of S and N availability. Plants were grown at 5, 45, or 125 mg·L-1 sulfate (SO42-), and 10, 50, 90, or 130 mg·L-1 N, in a factorial combination. Total bulb S, total and individual flavor precursors and their peptide intermediates in intact onion tissue were measured. To measure the effect of S and N on alliinase activity, flavor precursors were also measured in onion macerates. Sulfur and N availability in the hydroponics solution interacted to influence all flavor compounds except S-methyl-L-cysteine sulfoxide. Levels of S-methyl-L-cysteine sulfoxide were influenced by N and S levels in the solutions; however, no interaction was present. At the lowest SO 42- or N levels, most precursors and peptides measured were present in very low concentrations. When SO 42- or N availability was adequate, differences among flavor compounds were small. Results indicated that S fertility had a greater influence on trans-S-1-propenyl-L-cysteine sulfoxide (1-PRENCSO) accumulation, while N availability had a greater influence on S-methyl-L-cysteine sulfoxide levels. Flavor precursors remaining in the onion macerates revealed that the percentage of intact precursors hydrolyzed by alliinase were not significantly influenced by either SO 42- or N levels in the solutions, except for 1-PRENCSO, which was affected by N levels. Nitrogen and S fertility interacted to influence the flavor biosynthetic pathway and may need to be considered together when manipulating onion flavor compounds.