Intake of marine-based n-3 fatty acids (EPA, docosapentaenoic acid and DHA) is recommended to prevent CHD. Stearidonic acid (SDA), a plant-based n-3 fatty acid, is a precursor of EPA and may be more readily converted to EPA than α-linolenic acid (ALA). While transgenic soyabeans might supply SDA at low cost, it is unclear whether SDA is associated with CHD risk. Furthermore, associations of other n-3 fatty acids with CHD risk remain inconsistent. The present ancillary study examined the association of erythrocyte SDA as well as other n-3 fatty acids with the risk of CHD. In a prospective nested case–control study of the Physicians' Health Study, we randomly selected 1000 pairs of incident CHD with matching controls. Erythrocyte fatty acids were measured using GC. We used conditional logistic regression to estimate relative risks. Mean age was 68·7 (sd 8·7) years. In a multivariable model controlling for matching factors and established CHD risk factors, OR for CHD for each standard deviation increase of log-SDA was 1·03 (95 % CI 0·90, 1·18). Corresponding values for log-ALA and log-marine n-3 fatty acids were 1·04 (95 % CI 0·94, 1·16) and 0·97 (95 % CI 0·88, 1·07), respectively. In conclusion, the present data did not show an association among erythrocyte SDA, ALA or marine n-3 fatty acids and the risk of CHD in male physicians.