This paper studies the effect of food web structure on the extinction risk of species. We examine 793 different six-species food web structures with different number, position and strength of trophic links and expose them to stochasticity in a model with Lotka–Volterra predator–prey dynamics. The characteristics of species (intrinsic rates of increase as well as intraspecific density dependence) are held constant, but the interactions with other species and characteristics of the food web are varied. Extinctions of producer species occurred but were rare. Species at all trophic levels went extinct in communities with strong interactions as compared to communities with no strong interactions where only the secondary consumer went extinct. Extinction of a species directly involved in a strong interaction was more frequent than extinctions of species not directly involved in strong interactions (here termed direct and indirect extinctions, respectively). In model webs where both direct and indirect extinctions occurred, roughly 20% were indirect extinctions. The probability of indirect extinctions decreased with number of links. It is concluded that not just the presence of strong interactions but also their position and direction can have profound effects on extinction risk of species. Three principal components, based on 11 different food web metrics, explained 76.6% of the variation in trophic structure among food webs that differed in the number and position, but not strength, of trophic links. The extinction risk of consumer species was closely correlated to at least two of the three principal components, indicating that extinction risk of consumer species were affected by food web structure. The existence of a relationship between food web structure and extinction risk of a species was confirmed by a regression tree analysis and a complementary log-linear analysis. These analyses showed that extinction of consumer species were affected by the position of strong interactions and a varying number of other food web metrics, different for intermediate and top species. Furthermore, the degree to which the equilibrium abundance of a species is affected by a press perturbation is an indication of the risk of extinction that this species faces when exposed to environmental stochasticity. It is concluded that extinction risk of a species is determined in a complicated way by an interaction among species characteristics, food web structure and the type of disturbance.

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