Objectives : This study was designed to investigate the clinical characteristics and usefulness of comprehensive diagnosis of Yin-deficiency and heart rate variability in patients with burning mouth syndrome (BMS). Methods : We surveyed 30 burning mouth syndrome patients visiting the Oral Diseases Clinic of Kyung Hee University Oriental Medicine Hospital from April to September of 2011. The subjects were evaluated on self-assessed severity of burning mouth syndrome and xerostomia using visual analogue scale (VAS) score and Yin-deficiency condition (based on the 10-item Yin-deficiency questionnaire). Salivary function was measured by the unstimulated salivary flow rate (USFR), and heart rate variability (HRV) parameters were recorded by SA-2000E (Medicore Co., Ltd., Korea). Results : There were substantial significant positive correlations between burning sensation VAS scores in mouth and Yin-deficiency scores. There was significant negative correlation between xerostomia VAS score and USFR. Compared to the normal range of total power (TP) in HRV parameters, the burning mouth syndrome patients showed significant lower values of TP. Conclusions : The results of this study suggest that comprehensive diagnosis of Yin-deficiecny and HRV parameters are useful in diagnosing of burning mouth syndrome patients. Therefore, we assume that improvement of Yin-deficiency condition can be a potentially effective way to treat burning mouth syndrome.