This study was arranged to examine whether vitamin B12 deficiency may cause autonomic dysfunction. Time-domain and long-term frequency-domain heart rate variability parameters from 12 patients with pernicious anemia were compared to 12 age and sex matched controls. In B12 deficient patient group time-domain parameters; SDNN (100.4 +/- 37.86 vs. 131.91 +/- 26.94, P = 0.05), SDANN (87.00 +/- 37.77 vs. 118.83 +/- 26.22, P = 0.05) SD (39.41 +/- 13.32 vs. 53.41 +/- 15.39, P = 0.0221), rMSSD (21.41 +/- 10.00 vs. 28.5 +/- 8.42, P = 0.046) were significantly lower when compared to controls. Difference in pNN50 between groups were not statistically significant. In B12 deficient patients frequency-domain parameters; total power (23.08 +/- 9.89 vs. 34.75 +/- 9.56, P = 0.0078), low frequency power (13.5 +/- 6.57 vs. 22.75 +/- 7.25, P = 0.0069) and high frequency power (7.58 +/- 4.25 vs. 11.58 +/- 3.80, P = 0.0175) were significantly lower when compared to controls. It was concluded that B12 deficiency may cause autonomic dysfunction.