Objective. Hyperhomocysteinaemia is considered to be a risk factor for cardiovascular disease (particularly stroke) and has been implicated in recurrent miscarriage and osteoporotic fracture, recognized manifestations of coeliac disease (CD). The objective of this study was to compare plasma homocysteine levels and biomarker status of metabolically related B vitamins (folate, vitamin B-12, B-6 and riboflavin) in treated and untreated CD patients and healthy controls. Material and methods. CD patients attending a clinic for either initial or follow-up biopsy (at least 12 months after commencing a gluten-free diet) were categorized into three groups: 1) newly diagnosed (untreated; n=35); 2) persistent villous atrophy (VA) at follow-up (n=24) or 3) recovered VA at follow-up (n=41). Blood samples were analysed for plasma homocysteine, serum and red cell folate and serum vitamin B-12 levels, and for plasma pyridoxal 5-phosphate (PLP, vitamin B-6) and riboflavin (vitamin B-2) status. Results. Homocysteine concentrations were significantly higher (p=0.05) and red cell and serum folate significantly lower (p<0.001) in untreated patients compared with controls, while all three reached normal levels in recovered VA patients. Although untreated and persistent VA patients tended to have lower B-12 levels, these did not reach significance. There was no evidence of compromised B-6 or riboflavin status, even in untreated CD patients. Homocysteine concentrations were inversely associated with both serum (r=-0.421; p<0.001) and red cell (r=-0.459; p<0.001) folate and with serum vitamin B-12 (r=-0.353; p=0.001). Conclusions. Gluten exclusion in CD improves folate status and normalizes homocysteine concentrations. Reducing the risk of homocysteine-related disease may be another reason for aggressive diagnosis and treatment of CD.