The objective of the present study was to assess the impact of ethnicity on hair trace element content in Han and aboriginal inhabitants of Hualien in Taiwan. Fifty Han (female/male = 35/15) and 50 aboriginal (female/male = 40/10) Hualien inhabitants aged 40–60 years were involved in the present study. Anthropometric data and dietary patterns were recorded. Hair mineral, essential, and toxic trace element levels were assessed using inductively coupled plasma mass spectrometry at NexION 300D (PerkinElmer Inc., USA) equipped with ESI SC-2 DX4 autosampler (Elemental Scientific Inc., USA). No group difference in gender, age, body weight, height, or physical activity was observed. Fish intake was more frequent in Han inhabitants, whereas aborigines consumed significantly more nuts. Indigenous people were characterized by higher hair Al (45%), Ca (threefold), Co (71%), Fe (twofold), I (74%), K (60%), Mg (2.5-fold), Na (62%), P (6%), Sn (78%), and V (46%) content. In turn, Han Hualien inhabitants had higher hair Be (twofold), Li, Se, Si levels as compared to indigenous counterparts. Multiple regression analysis demonstrated that ethnicity was significantly associated with hair Ca (β = 0.302), Mn (β = 0.284), P (β = 0.387), and Se (β = − 0.310) levels after adjustment for other confounders. At the same time, the overall models were significant for Ca, Mn, Se, and As. The obtained data may provide a background for monitoring and correction of trace element status in patients of different ethnic groups. However, further detailed studies are required to highlight the mechanisms underlying the observed associations. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.