The clinical presentation of patients with vitamin B-12 deficiency varies in a spectrum ranging from haematological disorders to neuropsychiatric diseases. In rare cases, orthostatic hypotension, impotence, constipation and urinary retention have been attributed to autonomic nervous system dysfunction due to vitamin B-12 deficiency. The aim of this study was to evaluate the effect of vitamin B-12 deficiency on autonomic nervous system function by studying gastric emptying times (T-1/2). Twenty patients with newly diagnosed vitamin B-12 deficiency and 12 control patients with gastritis and normal vitamin B-12 levels were enrolled in this study. Gastroduodenoscopy, endoscopic biopsy, histopathological evaluation of the biopsy specimens and radionuclide gastric emptying studies were performed. After vitamin B-12 replacement therapy for 3 months, radionuclide gastric emptying studies were repeated. Mean gastric emptying T-1/2 in patients before and after treatment and in controls were 103.83 +/- 48.80 min, 90.00 +/- 17.29 min and 74.55 +/- 8.52 min, respectively. The difference in mean gastric emptying T-1/2 between patients before treatment and controls was statistically significant (P<0.01). The statistically significant difference persisted after vitamin B-12 treatment (P<0.05), though mean gastric emptying T1/2 was somewhat shorter. There were no positive or negative correlations between gastric emptying T-1/2 and the following parameters: haemoglobin, vitamin B-12 level and Helicobacter pylori positivity. In conclusion, gastric emptying T1/2 was prolonged in patients with vitamin B-12 deficiency and this prolongation was not corrected after vitamin B-12 replacement therapy. Although autonomic nervous system dysfunction due to vitamin B-12 deficiency rarely gives rise to clinical manifestations, latent dysfunction demonstrated by laboratory tests seems to be a frequent phenomenon. The level of vitamin B-12 does not correlate with the degree of autonomic nervous system dysfunction measured by radionuclide gastric emptying studies.