Objective:To compare the dietary habits of children living in northern villages and in the capital of Greenland, given the reported transition from traditional to westernised diet in adults over recent decades, and to explore the association between consumption of marine mammals and fish (MMF) and the children’s metabolic profile and vitamin D status.Design:Children answered an FFQ encompassing sixty-four individual food types pooled into six food categories. Their pubertal stage, body fat, fitness level, metabolic profile (non-HDL-cholesterol, glycated Hb, insulin, glucose, high-sensitivity C-reactive protein) as well as serum 25-hydroxyvitamin D (25(OH)D) concentration were evaluated.Setting:Siorapaluk and Qaanaaq (north of Greenland) and Nuuk (west).Participants:Children aged 6–18 years (n 177).Results:MMF were most frequently eaten by children from Siorapaluk (mean (sd): 73·4 (14·1) times/month), followed by children from Qaanaaq (37·0 (25·0) times/month), and least often eaten by children from Nuuk (23·7 (24·6) times/month; P < 0·001). Children from Qaanaaq consumed ‘junk food’ more frequently (P < 0·001) and fruits and vegetables less frequently (P < 0·01) than children from Nuuk. MMF consumption was positively associated with serum 25(OH)D concentration (P < 0·05), but the overall prevalence of vitamin D deficiency was high (18 %). No association was found between MMF consumption and metabolic parameters.Conclusions:The dietary transition and influence of western diets have spread to the north of Greenland and only the most remote place consumed a traditional diet highly based on MMF. We found no strong associations of MMF consumption with metabolic health, but a positive association with vitamin D status.