Although the effects of dietary polyunsaturated fatty acids (PUFA) are well-known in the heart and brain, little is known about oxylipins, their bioactive lipid metabolites. To provide fundamental data on these oxylipin profiles, and the effects of dietary PUFA and sex on these profiles, weanling female and male Sprague-Dawley rats were given diets modified in oil composition to provide higher levels of α-linolenic acid, eicosapentaenoic acid, docosahexaenoic acid or linoleic acid, compared to control diets. Dietary PUFA mainly altered the levels of their own oxylipins, but also affected others. N-6 PUFA derived oxylipins were reduced by dietary n-3 PUFA in the heart, but not the brain, which generally was less resistant to diet-induced changes in oxylipins. Oxylipins were generally higher in females in heart but higher in males in brain. These data provide fundamental data that will inform studies on the roles of oxylipins in heart and brain.