The winter diet of the great cormorant (Phalacrocorax carbo) was studied by means of examining regurgitated pellets, individual fish bones and fish remains collected from below the roosting trees in two sites on the River Vltava in Vyšší Brod and at Slapy Reservoir, Czech Republic, and by analysis of stomach contents of birds shot on the River Vltava in Prague. Using diagnostic bones (os pharyngeum, dentale, maxillare, praeoperculare) and own linear regression equations between measured dimension of the diagnostic bone and fish total length (LT), a total of 1152 fish of 22 species and 6 families were identified in the diet of great cormorants and their sizes were reconstructed. At all three localities on the main stream of the River Vltava, roach (Rutilus rutilus), bream (Abramis brama), bleak (Alburnus alburnus), European chub (Squalius cephalus), European perch (Perca fluviatilis) and ruffe (Gymnocephalus cernuus) made up at least 74.2 % of the cormorants’ diet. A great potential for fish stock losses was identified for the River Vltava at Vyšší Brod and in Prague where the loss of fish due to overwintering great cormorants was estimated to be 22 kg ha–1 and up to 79 kg ha–1 respectively, i.e. belonging among the highest ever published figures for fish withdrawal caused by great cormorants from any inland waters (carp fishponds excluded). Most probably, both great cormorants and anglers are responsible for the decrease in catches of brown trout (Salmo trutta m. fario) and grayling (Thymallus thymallus) from the River Vltava in Vyšší Brod.