The purpose of the present study was to investigate and compare the clinical characteristics of burning mouth syndrome (BMS) patients with bilateral and unilateral symptoms. Of 769 patients with oral burning sensation, 421 patients with primary BMS were included. Among them, 324 patients who complained of oral symptoms on both sides of the oral cavity were assigned to the bilateral group and 97 patients who complained of symptoms only on one side of the oral cavity were assigned to the unilateral group. Clinical characteristics, psychological status, and salivary secretion were compared between the two groups. There were no significant differences in the mean age, sex ratio, unstimulated and stimulated salivary flow rates, or duration of symptoms between the two groups. The bilateral group had higher levels of psychological distresses compared with the unilateral group. The bilateral group had higher prevalence rates in burning, taste alteration, and xerostomia than the unilateral group. The proportion of patients who considered dental procedures as an initiating factor of BMS symptoms was higher in the unilateral group than in the bilateral group. Conclusively, BMS patients with bilateral and unilateral symptoms had different clinical characteristics, suggesting that the neuropathic mechanisms in these two groups are different.