A key challenge in ecology is to find ways to obtain complete and accurate information about the diets of animals. To respond to this challenge in seabirds, traditional methods (usually stomach content analysis or observations of prey at nests) have been supplemented with indirect methods or molecular trophic markers. These techniques have the potential to extend the period of investigation outside the few short months of breeding and avoid biases. Here, we use an analysis of fatty acids (FAs) and fatty alcohols (FALs) from blood, adipose tissue and stomach oil to investigate how the diets of male and female common guillemots (Uria aalge), black-legged kittiwakes (Rissa tridactyla) and northern fulmars (Fulmarus glacialis) differed through the sampling period (prelaying and breeding season) and by sex. Diets of both sexes of all three species generally varied across the season, but sex differences were apparent only in fulmars during prelaying. Our study shows that FA/FAL analysis can provide significant insights into diets of seabirds, in particular periods of the annual cycle which are not readily studied using traditional methods.