Limited data are available on the fatty acid (FA) composition of circulating lipids and the associations with diet, physiological and pathological conditions, due to the complexity and costs of the analytical process. The aim of our study was to evaluate the FA composition in 108 healthy subjects and to correlate the data with gender, pregnancy, dietary habits, lifestyle, and short-term controlled intake of n-3 FA, using an innovative analytical approach for the collection and processing of blood samples. Ten subjects were also supplemented with n-3 polyunsaturated FA as smoked salmon or capsules for 3 weeks. The resulting blood FA composition was affected by gender, pregnancy, diet and smoking. The data indicate that this new analytical methodology is suitable for assessing associations between circulating FA and various parameters in large population groups, and is applicable to epidemiological studies and in the assessment of the effects of controlled FA supplementation in clinical studies.