Recent studies have suggested that untreated coeliac disease is associated with lower total cholesterol than in the general population while the effect of treatment with a gluten-free diet on the cholesterol profile of clinically apparent coeliac disease is not known. We measured the cholesterol profile at diagnosis, and compared this with Health Survey for England figures, and again following 12 months treatment with a gluten-free diet in 100 consecutive adults with coeliac disease attending the Royal Hallamshire Hospital, Sheffield, UK. The mean total cholesterol was 4·84 (sd 1·2) mmol/l in adults (mean age 51 (sd 16) years) newly diagnosed with coeliac disease. At diagnosis of coeliac disease, men had 21 % lower and women had 9 % lower mean total cholesterol in comparison to the general population (difference in age-adjusted mean total cholesterol − 1·09 mmol/l (95 % CI − 0·97, − 1·21); − 0·46 mmol/l (95 % CI − 0·24, − 0·68), respectively). There was no change in mean total cholesterol following treatment. However, there was a small but statistically significant increase of 0·12 mmol/l (95 % CI 0·05, 0·18) in the mean HDL-cholesterol. Total cholesterol was lower at diagnosis in coeliac patients than in the general population and did not increase with 1 year of a gluten-free diet while HDL-cholesterol increased following treatment. Any increase in risk of IHD or stroke in people with coeliac disease is unlikely due to an adverse cholesterol profile either before diagnosis or after treatment with a gluten-free diet.