Overt vitamin B12 deficiency is associated with an increased risk of depression, however, the mechanism is not well established. Depression, though is often treated with selective serotonin reuptake inhibitors (SSRIs), with the assumption that there is an imbalance in serotonin production. Functional vitamin B12 deficiency is common in those with functional vitamin B2 deficiency. In the current study, glutaric acid, a marker of functional B2 deficiency has been compared with various markers of the melatonin/serotonin/kynurenine pathway. A graded, bi-phasic response was observed whereby in low level functional B2 deficiency there was a huge increase in the production of serotonin, however as levels of functional B2 deficiency increased serotonin production was reduced and a large increase in Quinolinic acid was observed. The data suggests that correction of the serotonin/melatonin synthesis pathway may require supplementation with Iodine, Selenium, vitamin B2 and methylcobalamin.