Abstract Background Elevated serum total homocysteine (tHcy) is associated with an increased risk of cardiovascular disease. Homocysteine levels may be influenced by dietary habits. The aim of the present study was to determine the effects of a vegetarian diet on some of the cardiovascular risk factors in Turkish females. Method The study was conducted on 26 vegetarian and 26 omnivore females. Serum tHcy, folate, vitamin B12 and lipids were determined and dietary data were assessed using a 4-day food intake record at two time points. Results Compared with omnivores, vegetarians had higher plasma tHcy, 10.8 ± 3.72 versus 12.6 ± 5.97, (P < 0.05) and folate (P < 0.05) levels. The prevalence of hyperhomocysteinaemia was higher in vegetarians than in omnivores (34.6% versus 12.0%). In addition, serum vitamin B12 levels were lower in vegetarians than in omnivores (P < 0.05). In vegetarians, significant inverse correlation was found between tHcy and serum vitamin B12 levels (r = −0.969, P = 0.001). Conclusion The higher prevalence of mild hyperhomocysteinaemia in vegetarians indicated a diminished protective effect of vegetarian nutrition in cardiovascular disease prevention.