The influence of two sampling protocols on diet determination of two marine predators, the Gentoo penguin Pygoscelis papua and Antarctic fur seal Arctocephalus gazella, was investigated. The collection of diet samples on three occasions over a two week period was compared with collecting all samples during a single session, as current CEMP monitoring protocols recommend. Some differences in the mass of food recovered from penguins were found but this was attributed to the mass of penguin sampled. There were no differences in diet composition between protocols and although body mass was a significant determinant of the mean length of krill Euphausia superba recovered from penguins, there were no differences between sampling protocols. This study has shown that differences between sampling frequencies are small and a variety of sampling protocols can produce results acceptable for inter-annual monitoring. Mass of sampled individuals can account for significant variation and should be recorded, especially if sampling frequencies and sizes are low.