Functional vitamin B12 markers were compared with serum vitamin B12 levels in 350 individuals, to see if there was a correlation between markers of vitamin B12 deficiency, and the actual levels of vitamin B12 in serum. No correlation was found between normal to elevated levels of vitamin B12 and urinary methyl malonic acid, or vitamin B12 deficiency associated neurotransmitter metabolites. Hence, whilst serum vitamin B12 levels were normal or elevated these individuals had Paradoxical B12 deficiency. Vitamin B12 deficiency markers were, however, correlated with markers of vitamin B2 deficiency, suggesting that the vitamin B2 deficiency had led to elevated levels of vitamin B12, which was largely inactive. Given the role in energy metabolism, correct diagnosis of vitamin B12 deficiency is essential. The mechanism is discussed.