Background: Magnesium plays an important role in carbohydrate metabolism. Hypomagnesaemia associated with diabetes mellitus may play a role in the pathogenesis of atherosclerosis. Aim: The aim of this study is to explore the influence of serum magnesium (Mg) level on concentration of serum lipids in Sudanese diabetes mellitus (DM) patients Materials and methods: A case control study included 179 diabetic patients and 200 diabetes-free apparently healthy controls, recruited from Jabir Abu Eliz centre for diabetic patients, Khartoum –Sudan, between May and September 2013. Serum magnesium (Mg) and serum lipids, consisting of triacylglycerol (Tg), cholesterol (Chol) and high density lipoprotein (HDL) were determined in both cases and controls. Results: Both serum Mg and HDL-C showed low levels in diabetic patients, while LDL-C was higher in the control group as compared to the diabetics. A strong positive correlation was noticed between serum Mg and HDL-C in diabetic patients, r=0.716 and P ˂0.05 Conclusion: Level of serum Mg has strong influence on serum lipids in diabetes mellitus patients, and hypomagnesaemia associated with diabetes can be a risk factor for CHD in diabetics.