In this study, 14 well-adapted genotypes of pistachio (Pistachio vera L.) grown in Diyarbakır (Southeastern Turkey) and 15 walnut (Juglans regia L.) genotypes grown in Erzincan (Eastern Turkey) have been studied. Pistachio genotypes contained 8.16-9.33% palmitic acid, 0.54-0.68% palmitoleic acid, 2.35-4.21% stearic acid, 67.81-76.82% oleic acid, 9.42-18:32% linoleic acid, 0.27-0.38% linolenic acid and 0.19-0.33 % arachidic acid. The range of selenium, α-tocopherol, γ-tocopherol, δ-tocopherol, α-tocotrienoid, γ-tocotrienoid and total carotenoid of these promising genotypes were found to be between 11.44 and 190.71 ng/g, 1.36 and 26.93, 36.17 and 170, 0.45 and 2.61, 0.96 and 3.76, 2.33 and 37.72 and 1.01 and 4.93 mg/kg, respectively. Linoleic acid ranging from 43.19% to 53.16% was the most abundant fatty acid in 15 pomologically selected walnut genotypes, followed by oleic and linolenic acids (31.91% and 11.46%, respectively). Their selenium contents ranged between 7.25 and 57.67 ng/g. γ-Tocopherol was the predominant tocopherol in walnut genotypes. Pistachio and walnut genotypes with higher unsaturated fatty acids, tocopherols and selenium contents may be valuable for nutritional breeding efforts.