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Data on bone mineral density (BMD) in living Inuit are limited and BMD measurements in Arctic Inuit using Dualenergy X-ray Absorptiometry (DXA) are lacking. Ethnicity may be important for bone mass. The aim of this study was to validate DXA in rural Arctic Greenland, to measure BMD in Greenland Inuit and Caucasians, and to estimate the importance of ethnicity for BMD. We measured the BMD in 80 healthy subjects living in Ilulissat and Saqqaq in North Greenland twice in both distal forearms and in both heels using peripheral DXA (pDXA). Participants were stratified by origin (Inuit[settlement])/Caucasians, n = 33 /28), gender (men/women, n = 37/43), and age (30–39/40–49, n = 32/48). Caucasians were bigger than Inuit (men/women, height p < 0.001/p < 0.001; weight p = 0.01/p = 0.026), but had similar BMI (p = 0.42/0.70). Triplicate pDXA measurements showed individual CV% = 0.16–1.79%; overall CV% = 1.1% (forearm)/1.0% (heel). Data followed the normal distribution (p = 0.65–0.99) with identical variances between Inuit and Caucasians (p = 0.12–0.63). Mean BMD in right forearm/left forearm/right heel/left heel was: Inuit men 0.570/0.568/0.549/0.536 g/cm2; Inuit women 0.484/0.474/0.473/0.464 g/cm2; Caucasian men 0.580/0.570/0.646/0.638 g/cm2; Caucasian women 0.495/0.496/0.552/0.553 g/cm2. An ethnic difference in heel BMD (p < 0.001) disappeared when adjusted for weight (p = 0.30). No difference was found in forearm BMD.In conclusion, pDXA is feasible and reliable in rural Greenland. Ethnic differences in BMD are small and may reflect differences in body size.