We evaluated the association between dietary estimates of fatty acid (FA) consumption and type 2 diabetes (T2D) risk in the French E3N (Etude Epidémiologique auprès des femmes de la Mutuelle Générale de l’Education Nationale) cohort. In total, 71 334 women without diabetes at baseline were followed up from 1993 to 2011. Diabetes was identified using questionnaires and drug-reimbursement claims, and incident cases were validated. FA consumption in 1993 was estimated from a validated dietary questionnaire. Cox regression estimated hazard ratios (HR) and 95 % CI of diabetes risk, comparing the upper tertile group with the lowest. High n-3 PUFA consumption was associated with T2D even after adjustment for confounders, including other FA and BMI (HR 1·26; 95 % CI 1·13, 1·41; upper tertile compared with lowest). Upon stratification by overweight (BMI≥25 kg/m2)/non-overweight, a positive association between total PUFA consumption and T2D was observed, but it was restricted to non-overweight women (HR 1·22; 95 % CI 1·05, 1·42), whereas n-3 PUFA consumption was associated with increased T2D risk in both BMI strata (BMI<25 kg/m2: HR 1·19; 95 % CI 1·01, 1·40 and BMI≥25 kg/m2: HR 1·38; 95 % CI 1·20, 1·59). Within the n-3 PUFA, high DPA (HR 1·41; 95 % CI 1·23, 1·63) and α-linolenic acid (ALA) intakes were associated with increased T2D risk, but the effects of ALA were restricted to overweight women (HR 1·17; 95 % CI 1·01, 1·36). Within the n-6 PUFA, only arachidonic acid (AA) intake was associated with T2D risk (HR 1·49; 95 % CI 1·33, 1·66). The associations with DPA and AA persisted even after adjustment of their principal source in this cohort, the consumption of meat. The effects of PUFA are heterogeneous within the FA group. Intake of DPA and AA may contribute to T2D development.