This study was conducted to characterize shortday onions of 3 pungency levels with regard to the composition of flavor related compounds. A total of 9 onion breeding lines/cultivars were selected, per each of low, medium, and high pungency level, with pyruvic acid contents of 1.9 to 2.8, 4.8 to 5.4, and 7.2 to 8.3 micromoles/mL, respectively. The contents of flavor precursors (S-1-propenyl-L-cysteine sulfoxide [1-PeCSO] and S-methyl-L-cysteine-sulfoxide [MCSO]), free amino acids, free sugars, soluble solids (SSC), and total sulfur (S) in onion bulbs were measured. The flavor precursor contents ranged from 0.03 to 0.16 mg/g fresh weight (FW) for MCSO, 0.07 to 0.65 mg for 1-PeCSO, and 0.12 to 0.77 mg in total, and precursor contents increased with the pungency levels. Onions of different pungency levels did not differ in the contents of individual or total free amino acids, and the most abundant amino acids were glutamine and arginine. The total sugar contents ranged from 50 to 75 mg/g FW, and total S contents (3.5 to 5.1 mg/g dry weight) were not correlated with the pungency levels. However, pungency levels were correlated inversely with bulb weight and positively with SSC, presumably by the effect of dilution. This study indicates that onion pungency is primarily determined by the content of flavor precursor compounds and not by total S, total sugars, or individual/total free amino acids in shortday bulbs.