Onion bulbs accumulate fructans, a type of soluble carbohydrate associated with lower rates of colorectal cancers. Higher fructan concentrations in bulbs are correlated with higher pungency, longer dormancy, and greater onion-induced antiplatelet activity (OIAA). We analyzed replicated field trials of a segregating family for types and concentrations of soluble carbohydrates in onion bulbs 90 days after harvest. Means were adjusted using dry weight as the covariant to reveal highly significant (P < 0.001) differences among parents and families for glucose, fructose, sucrose, and the fructans 1-kestose, neokestose, and (6G,1)-nystose. Fructan concentrations showed significant (P < 0.05) phenotypic correlations with each other and with sucrose, pungency, and OIAA. These observations are consistent with the hypothesis that onion bulbs accumulating fructans take up or retain less water, concentrating both soluble carbohydrates and thiosulfinates responsible for pungency and OIAA. Interval mapping of family means from the covariant analyses revealed regions on linkage groups A and D significantly (LOD > 2.68) affecting soluble carbohydrate concentrations. The enzyme catalyzing the first step of fructan polymerization, 1-sucrose-sucrose fructosyltransferase (1-SST), mapped independently of these genomic regions. One region on linkage group D near an acid-invertase gene was significantly (LOD = 3.45) associated with sucrose concentrations. This study reveals that the accumulation of sucrose in stored onion bulbs may allow for the combination of sweeter flavor with significant OIAA.