In relapsing-remitting multiple sclerosis (RRMS), the autonomic nervous system (ANS) can be affected and may deteriorate the disability of patients. Evaluation and management of autonomic dysfunction may improve quality of life of patients. We aimed to assess the autonomic dysfunction via heart rate variability (HRV) along with serum tumor necrosis factor-α (TNF-α) and interleukin-10 (IL-10) levels and disclose the correlations between HRV and levels of these two chief biomarkers in the immunopathology of MS, if any. Thirty-six consecutive RRMS patients who had an EDSS score of 0-3 EDSS, not in the relapse period and receiving interferon beta treatment were compared with age and gender-matched 37 healthy subjects in terms of HRV, serum TNF- and IL-10 levels. ANS was evaluated by frequency-based HRV analysis. TNF-α and IL-10 levels in serum were measured by the ELISA method. The mean serum TNF-α level was found to be higher in the RRMS group compared to the controls (p=0.010) but not the IL-10 (p=0.726). HRV parameters were significantly lower in the RRMS patients compared to the controls. No correlation was found between the inflammatory markers and HRV parameters in patients with MS. We found high levels of TNF-α, known to correlate with the severity and progression of MS, along with low levels of HRV in our patient group when compared with controls. Our results show that neurodegeneration and autonomic dysfunction can be present even in patients with RRMS with a low level of disability.