Data concerning the long-term effects of n-3 and n-6 PUFA on disease control and development of complications in diabetic patients are inconsistent. The relationship between plasma phospholipid PUFA and total mortality in type 2 diabetes is unknown. The present study aims to investigate the association between plasma phospholipid fatty acid relative concentrations expressed as weight percentage and total mortality in patients with type 2 diabetes. Mortality rates were evaluated at 5, 10, 15 and 20 years in patients with newly diagnosed diabetes (n 323) and matched non-diabetic controls (n 200) recruited from the Nord-Trøndelag Health (HUNT) Study, Norway. Kaplan–Meier survival curves were constructed and Cox regression analysis was used to calculate hazard ratios (HR) adjusted for biochemical and clinical covariates. After 10 years of follow-up, EPA in the diabetic population was negatively associated with total mortality, with an HR at the fifth quintile of 0·47 (95 % CI 0·25, 0·90) compared with the first quintile. In contrast, DHA was positively associated with total mortality, with an HR at the fifth quintile of 2·87 (95 % CI 1·45, 5·66). Neither EPA nor DHA was associated with total mortality in matched non-diabetic controls. In conclusion, plasma phospholipid relative concentrations of EPA were negatively associated, while those of DHA were positively associated with total mortality in diabetics. This difference in associations suggests a differential effect of EPA and DHA in patients with type 2 diabetes.