Concentrations of persistent organic pollutants (POPs) are high in Inuit living predominately on the traditional marine diet. Adverse effects of POPs include disruption of the immune system and cardiovascular diseases that are frequent in Greenland Inuit. We aimed to assess the association between exposure to POPs from the marine diet and inflammation, taking into account other factors such as vitamin D. We invited Inuit and non-Inuit living in settlements or the town in rural East Greenland or in the capital city Nuuk. Participants completed a food frequency questionnaire and donated a blood sample for measurement of the two markers of inflammation YKL-40 and hsCRP, 25-hydroxy-vitamin D, eleven organochlorine pesticides (OCPs), fourteen polychlorinated biphenyls (PCBs), one polybrominated biphenyl, and nine polybrominated diphenyl ethers (PBDEs) adjusted to the serum lipid content. Participants were 50 through 69 years old, living in settlements, town or city (n = 151/173/211; 95% participation rate). ΣOCP, ΣPCB and ΣPBDE serum levels were higher in Inuit than in non-Inuit (p<0.001/ p<0.001/ p<0.001), in older individuals (p<0.001/p<0.001/p = 0.002) and in participants with the highest intake of Greenlandic food items (p<0.001/p<0.001/p<0.001). Both YKL-40 and hsCRP serum levels were higher in Inuit compared to non-Inuit (p<0.001/p = 0.001), and increased with age (p<0.001/p = 0.001) and with the intake of Greenlandic food items (p<0.001/p = 0.002). Multivariate analysis conformed to a marked influence on both YKL-40 and hsCRP by ΣOCP (p<0.001/p<0.001) and ΣPCBs (p<0.001/p = 0.001) after adjusting for age, BMI, vitamin D, alcohol and smoking. POP levels were associated with the intake of the traditional Inuit diet and with markers of inflammation. This supports a pro-inflammatory role of POPs to promote chronic diseases common to populations in Greenland. These data inform guidelines on 'the Arctic dilemma' and encourage follow-up on the ageing Arctic populations.