Abstract Background Concerns have been raised on whether a gluten-free diet affects the cardiovascular risk profile of coeliac patients. Aims To assess changes of multiple cardiovascular risk factors in coeliac patients evaluated before and during a gluten-free diet. Methods Retrospective analysis of the effects of 1–5 years of gluten-free diet on indicators of cardiovascular risk and on distribution in cardiovascular risk categories in 715 coeliac patients. Results Compared to baseline, significant increases were found in body mass index (21.4±3.4 vs. 22.5±3.5; p<0.0001), total cholesterol (171.2±37.4mg/dL vs. 181.4±35.1mg/dL; p<0.0001), and γ-glutamyl transpeptidase (16.5±14.9 vs. 19.5±19.2U/L; p<0.0001). Significant reductions were found in serum triglycerides (87.9±49.5 vs. 80.2±42.8mg/dL; p<0.0001) and homocysteine (16.9±9.6 vs. 13.3±8.0μmol/L; p=0.018) during gluten-free diet. The proportion of patients included in an arbitrarily defined category of “lowest cardiovascular risk profile” decreased from 58% at baseline to 47% during gluten-free diet. Conclusions A gluten-free diet significantly affects cardiovascular risk factors in coeliac patients, but changes do not consistently point towards worse or better risk profiles, thus suggesting that the diet is unlikely to be atherogenic.