The aim of this study was to estimate the composition of the diet and size‐related changes in the prey selection of pikeperch and pike in L. Peipsi. A total of 591 pikeperches with a standard length (Sl) of 9–73 cm and 254 pikes (Sl = 25–105 cm) were sampled with a bottom seine and an experimental trawl in 1994–1996 and their stomach content analysed. The frequency of occurrence and number of prey fish per individual were used for the description of the diet. The recent diet of pikeperch and pike in the Lake Peipsi were not exactly the same, although smelt, ruffe and perch were the main prey fishes of both. Smelt was the commonest in the diet of pikeperch in contrast to ruffe that was mainly taken by pike.