During migratory endurance flights, which are energetically very demanding, migrants have to deal with prolonged elevated generation of reactive oxygen species (ROS). To limit the damaging actions that ROS have on lipids and proteins, migrating birds are known to upregulate their antioxidant defence system. However, there may be additional ways to limit oxidative damage incurred from flying. Migratory endurance flights are fuelled mainly with fatty acids (FAs), and the risk of their peroxidation (resulting in oxidative lipid damage) increases with the number of double bonds in a FA, with polyunsaturated FAs (2 or more double bonds, PUFAs) being most peroxidation-prone. By fuelling their flights with relatively few PUFAs, migratory birds could thus limit oxidative lipid damage. Within migratory birds, there is considerable variation in the length of their flights, with nocturnal migrants making lengthier flight bouts, thus more likely to experience lengthier periods of elevated ROS production, than diurnal migrants. However, whether migrants making lengthier flights incur more oxidative lipid damage is unknown. Neither is it known whether flight length and FA composition are associated. Therefore, we determined plasmatic malondialdehyde level, a marker of oxidative lipid damage, and FA composition of three nocturnal and two diurnal migrant species caught at an autumn stopover site. We found little inter-specific variation in malondialdehyde level, indicating that the amount of oxidative lipid damage was comparable across the species. In contrast, the species strongly differed in their plasmatic FA composition. The nocturnal migrants had significantly lower relative PUFA levels than both diurnal migrants, an effect mainly attributable to linoleic acid, an essential (strictly dietary) FA. Consequently, the susceptibility of plasmatic FAs to lipid peroxidation was significantly lower in the nocturnal than diurnal migrants. Because in birds, energy expenditure during flight decreases with the degree of FA unsaturation, we interpret our observation of lower PUFA levels in nocturnal migrants as support for the idea that utilizing PUFA-poor fuel can help migrating birds to curb oxidative lipid damage.