Vitamin B12, folate, and vitamin B6 are the main determinants of homocysteinemia. The vegan diet provides no vitamin B12, but also less strict forms of alternative nutrition may suffer from a deficit of this vitamin. The plasma homocysteine level was measured in alternative nutrition groups of adults (lacto- and lactoovovegetarians, n = 62; vegans, n = 32) and compared with the levels in a group consuming traditional diet (n = 59), omnivores). In the group of vegetarians the average homocysteine level is 13.18 vs. 10.19 μmol/l in omnivores; the frequency of hyperhomocysteinemia is 29 vs. 5% in omnivores. In the group of vegans the average homocysteine value is 15.79 μmol/l (53% of the individual values exceeded 15 μmol/l). Omnivores consume the recommended amount of methionine; however, in individuals consuming an alternative diet, the intake of methionine is deficient (assessed by food frequency questionnaire; lower content of methionine in plant proteins). Under conditions of lower methionine availability the remethylation pathway prevails; therefore, vitamin B12 and folate were evaluated in relation to the homocysteine level. The serum vitamin B12 levels are significantly lower in the alternative nutrition groups (214.8 pmol/l in vegetarians, 140.1 pmol/l in vegans vs. 344.7 pmol/l in omnivores); a deficit (<179.0 pmol/l) was found in 26% of the vegetarians and in 78% of the vegans vs. 0% in omnivores. The serum folate levels were within the range of reference values in all groups; however, they were significantly lower in omnivores. The results show that the mild hyperhomocysteinemia in alternative nutrition is a consequence of vitamin B12 deficiency.