The present study was undertaken to determine the fatty acid profile of seeds of pepper (Capsicum annuum L.) cultivars 'Yağ', 'Çetinel-150' and 'Bağcı Çarliston' as well as the relations between fatty acid profile, seed germination and vigour at various temperatures (15, 25 and 35 °C). In this study, the germination percentage and vigour, total oil and the fatty acid profile of seeds of pepper cultivars were determined. There were significant differences in seed germination and vigour among the cultivars. Linoleic (C18:2n-6) acid was the principal fatty acid followed by palmitic (C16:0), oleic (C18:1n-9) and stearic (C18:0) acids in all cultivars. The highest concentrations of linoleic (77.8%), oleic (10.4%), palmitic (10.6%) and stearic (2.5%) acids were determined in the cultivars 'Çetinel-150', 'Yağ' and 'Bağcı Çarliston', respectively, and miristic, margaric, gadoleic and behenic acids at an even lower content (<1%). In addition to simple correlation coefficients (r) between the total oil, fatty acid composition, and germination percentage and vigour of the pepper cultivars, similar results were obtained in stepwise multiple regression analysis. According to the stepwise multiple regression analysis, although results for vigour were similar to the results of germination, in addition to linoleic acid, the indirect effect of miristic, margaric, palmitoleic and gadoleic acids were determined for vigour. Research results demonstrated that the low or high amount of fatty acids in the tested cultivars may play a major role on germination and vigour at various temperatures. Moreover, the role of linoleic acid (C18:2n-6) on germination and vigour associated with temperature was more explicit than that of the other fatty acids.