As part of the rapid socio-cultural transition observed in Arctic populations, the Inuit diet is changing. We present original data derived from the baseline Inuit Health in Transition cohort study regarding biological levels of n-3 fatty acids and trans-fatty acids (TFA), lipids with opposite health effects found respectively in traditional marine diets and recently introduced low-quality imported foods. A total of 524 Inuit from the Disko Bay area (Greenland) and 888 Inuit from the fourteen communities of Northern Québec (Nunavik) participated in the study. We measured the fatty acid profile of erythrocyte (RBC) membrane phospholipids (PL) as a surrogate for individual intakes. Moreover, the contribution of store-bought foods to energy intakes was assessed through dietary questionnaires. Our results show that while n-3 fatty acid levels were slightly lower in Nunavik (9.4 % of RBC membrane PL) than in Greenland (12.1 %), TFA levels were on average nearly thrice as high in Nunavik Inuit (1.20 %) as they were in Greenlanders (0.43 %). Moreover, younger Nunavik Inuit accumulated higher intakes of TFA and lower intakes of n-3 fatty acids. Finally, the average proportion of energy derived from store-bought foods was high in both groups (77.5 % and 83.5 %), especially in youth. Our results call for action to rehabilitate and recover access to country foods and point to the importance for Nunavik and the entire circumpolar world to follow the example of Denmark and Greenland, which imposed a maximum content of 2 g/100 g fat on industrially produced trans-fats in 2003.