Abstract Background High total cholesterol and low HDL (high-density lipoprotein) cholesterol are important determinants of cardiovascular disease. Little is known about dyslipidemia among Turkish and Moroccan migrants, two of the largest ethnic minority groups in several European countries. This study examines ethnic differences in total and HDL cholesterol levels between Dutch, Turkish and Moroccan ethnic groups. Methods Data were collected in the setting of a general health survey, in Amsterdam, the Netherlands, in 2004. Total response rate was 45% (Dutch: 46%, Turks: 50%, Moroccans: 39%). From 1,220 adults information on history of hypercholesterolemia, lifestyle and demographic background was obtained via health interviews. In a physical examination measurements of anthropometry and blood pressure were performed and blood was collected. Total and HDL cholesterol were determined in serum. Results Total cholesterol levels were lower and hypercholesterolemia was less prevalent among the Moroccan and Turkish than the Dutch ethnic population. HDL cholesterol was also relatively low among these migrant groups. The resulting total/HDL cholesterol ratio was particularly unfavourable among the Turkish ethnic group. Controlling for Body Mass Index and alcohol abstinence substantially attenuated ethnic differences in HDL cholesterol levels and total/HDL cholesterol ratio. Conclusions Total cholesterol levels are relatively low in Turkish and Moroccan migrants. However part of this advantage is off-set by their relatively low levels of HDL cholesterol, resulting in an unfavourable total/HDL cholesterol ratio, particularly in the Turkish population. Important factors in explaining ethnic differences are the relatively high Body Mass Index and level of alcohol abstinence in these migrant groups.