Diet of the Great Cormorant (Phalacrocorax carbo) was studied in three coastal wintering areas (Axios and Evros Deltas, Messolonghi Lagoon) of Greece, in order to assess spatial differences and commercial value of prey. Thirteen birds were collected from the Axios Delta, 28 from the Evros Delta, and 16 from Messolonghi Lagoon. Pellets were collected from the Evros Delta (26) and Messolonghi Lagoon (30). A variety of fish taxa were found in the samples, but only one or two dominated in Great Cormorant’s diet, either by numbers or biomass. Grey mullets (Mugilidae and Golden Grey Mullet Liza aurata) were the most important prey by numbers and biomass in the Axios Delta; Giebel (Carassius auratus gibelio) dominated by numbers and biomass in the Evros Delta; whereas Boyer’s Sand Smelt (Atherina boyeri) was most important by numbers and Mugilidae by biomass at Messolonghi Lagoon. Differences found in diet between areas are probably due to differences in prey species composition and abundance. Fish of high commercial value contributed in low proportions in Great Cormorant’s diet, by numbers and biomass, being highest at Messolonghi Lagoon (22.4% by numbers, pellets; 11.5% by biomass, stomachs). The small overlap between the bird’s diet and valuable prey suggests minimal competition with fisheries.