The purpose of this study was to test the autonomic nervous system function of patients with vitamin B12 deficiency (megaloblastic anemia) by measuring heart rate variability (HRV). The study population consisted of 17 vitamin B12 deficient patients and 15 age- and sex-matched normal volunteers. HRV was measured by power spectral analysis from which power of the low frequency (LF) peak (0.04-0.15 Hz), normalized units of the LF peak (LFNU), power of the high frequency (HF) peak (0.15-0.4 Hz), normalized units of the HF (HFNU), and ratio of power of LF to power of HF (LF:HF) were calculated. Vitamin B12 deficient patients had lower LF, LFNU, HF, HFNU, and LF:HF ratio than normal volunteers (P < 0.05). Decreases in sympathetic indices (LF and LFNU) were greater than those measured in parasympathetic indices (HF and HFNU). All HRV parameters correlated positively with the level of vitamin B12 (P < 0.001) and negatively with the duration of disease (P < 0.001). After vitamin B12 replacement the HRV parameters of patients and controls became comparable (P > 0.05). Our data suggest that autonomic sympathetic and parasympathetic nervous activities are decreased in patients with vitamin B12 deficiency, an abnormality that can be corrected by vitamin B12 replacement therapy.