Clinical studies have shown that hyper-homocysteinemia is a potent independent risk factor for cardiovascular diseases, and many different methods have been investigated for lowering it in hemodialysis (HD) patients. Our study investigated the effect of Vitamin B 12 supplementation on serum homocysteine levels in these patients. This randomized trial was conducted on 140 HD patients. They were randomly distributed by lottery method into two groups: intervention and control. In the intervention group, 100 μg/mL of Vitamin B 12 was intravenously injected two times a week, for eight weeks. No intervention was performed in the control group. Serum levels of homocysteine, hemoglobin (Hb), and hematocrit (Hct) were measured at the beginning and again after eight weeks (2 months) of treatment. About 91% of the patients had hyperhomocysteinemia (serum homocysteine >15 μmol/L). The median baseline levels of serum homocysteine in the intervention and control groups were 31.9 and 26.9 μmol/L, respectively (P = 0.1). After eight weeks, the median homocysteine level reduced significantly in the Vitamin B 12 group to 22.2 versus 28.4 μmol/L in control group (P = 0.006). The mean Hb and Hct also changed significantly during our study (12.3 vs. 11.4 g/dL; P = 0.003 and 37.9 vs. 35.3%; P = 0.02, respectively). Our results demonstrated the existence of a statistical negative relationship between Vitamin B 12 and serum levels of homocysteine. Detailed investigations with larger sample sizes and longer-term use of Vitamin B 12 are recommended.