Objectives: The aim of this study was to investigate the usefulness of a comprehensive diagnosis of yin-deficiency and heart rate variability in halitosis patients. Methods: We surveyed 62 halitosis patients visiting the Halitosis Clinic in the Kyung Hee University Oriental Medicine Hospital from August 2010 to April 2011. The subjects were evaluated on self-assessed severity of halitosis 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 halitosis, xerostomia VAS scores and yin-deficiency scores. There was significant negative correlation between xerostomia VAS score and USFR. Compared to the normal USFR group (USFR>0.1$m{ell}$/min), the decreased USFR group (USFR${leq}0.1m{ell}$/min) showed significant lower values of Total Power (TP), Lower Frequency (LF), and High frequency (HF). Conclusions: The results of this study suggest that the comprehensive diagnosis of yin-deficiency and HRV are useful in diagnosing of halitosis patients with xerostomia. Therefore, we assume that improvement of yin-deficiency condition can be a potentially effective way to treat halitosis with xerostomia.