Avian botulism is a fatal disease of birds caused by ingestion of neurotoxins produced by Clostridium botulinum type C and is now recognized as the most common cause of death in waterbirds worldwide. Although tens of species have been reported to suffer from avian botulism, it remains unknown which ecological factors primarily determine inter-specific variation in the incidence of this disease. We hypothesized that an exposure of birds to botulin may largely depend on their foraging niche, as the toxin is available mostly at the sediment surface, especially during the carcass-maggot stage of botulism epizootics. To test this hypothesis we used capture-recapture methods to estimate mortality of two shorebird species differing in bill morphology and foraging niche, wood sandpiper Tringa glareola (short bill, surface-feeding) and common snipe Gallinago gallinago (long bill, deep probing), during a major avian type C botulism outbreak in central Poland. All the reported cases of shorebird mortality were attributed to botulism and we found large differences in daily survival rates of both species (0.87 and 0.99 in wood sandpipers and common snipe, respectively). Even assuming much shorter stopover duration of wood sandpipers, survival rate over the entire stopover period was estimated at 0.57 in the wood sandpiper and at 0.90 in the common snipe. To our knowledge, this is the first non-circumstantial evidence that relatively minor differentiation of foraging niche may have a major impact on the incidence of avian botulism in birds. Our data might also suggest that, on the evolutionary time scale, avian type C botulism may constitute a strong selective pressure acting on foraging niches of shorebirds, and possibly other waterbirds.