The aim of this study was to determine the levels of proinflammatory tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) cytokines in whole unstimulated saliva in subjects with burning mouth syndrome (BMS) before and after treatment with low-level laser therapy (LLLT). BMS is characterized by a continuous, painful burning sensation in a clinically normal-appearing oral mucosa. A sample consisting of 40 consecutive subjects was selected on a voluntary basis from the pool of patients who presented for diagnosis and treatment of BMS at the Oral Medicine Unit of the Faculty of Medicine of the University of Rijeka. For determination of salivary levels of TNF-α and IL-6, ELISA (Sigma Immunochemicals, St. Louis, MO, USA) was performed to determine the salivary levels of TNF-α and IL-6. After 4 weeks of LLLT, the salivary levels of TNF-α and IL-6 in the experimental group decreased significantly (p < 0.001). There was no significant difference in the experimental group regarding visual analogue scale.