Dietary exposure to trans-fatty acids (TFA) is likely to be high among Canadian Inuit; yet no data are available on the physiological effects of TFA in this population. The purpose of the present study was to assess the association between TFA and plasma lipid profiles in Inuit men and women living in Nunavik (Québec, Canada). In a cross-sectional, population-based survey, a total of 795 Nunavik Inuit eligible participants gave a blood sample. Exposure to TFA was assessed by their relative proportion in erythrocyte membrane. We performed multiple regression analysis using plasma lipids or their linear combinations as the dependent variables and TFA as the main predictor, adjusting for potential confounders. The associations varied markedly between the sexes and according to age. In men (n 357, aged 36.3 (sd 14.3) years, TFA 1.24 (sd 0.54) %), TFA tended to be negatively associated with HDL-cholesterol (HDL-C), apoA1 and LDL particle size, and positively associated with non-HDL-C, LDL-cholesterol (LDL-C), apoB100, the apoB100:apoA1 ratio and the ratios of total cholesterol (TC), LDL-C and TAG to HDL-C. No such trends were observed in women (n 438, aged 37.0 (sd 14.1) years, TFA 1.16 (sd 0.54) %), except for HDL-C and apoA1 in women aged 50 years and more. These results suggest that TFA could raise the risk of CHD in Inuit men at least through their physiological effects on plasma lipids. The differential associations reported in pre- and postmenopausal women need to be reproduced in other populations and in experimental studies addressing the influence of sex hormones in response to dietary fats.