Abstract. Independent of the ongoing acidification of surface seawater, the majority of the calcium carbonate produced in the pelagial is dissolved by natural processes above the lysocline. We investigate to what extent grazing and passage of coccolithophorids through the guts of copepods and the food vacuoles of microzooplankton contribute to calcite dissolution. In laboratory experiments where the coccolithophorid Emiliania huxleyi was fed to the rotifer Brachionus plicatilis, the heterotrophic flagellate Oxyrrhis marina and the copepod Acartia tonsa, calcite dissolution rates of 45–55%, 37–53% and 5–22% of ingested calcite were found. We ascribe higher loss rates in microzooplankton food vacuoles as compared to copepod guts to the strongly acidic digestion and the individual packaging of algal cells. In further experiments, specific rates of calcification and calcite dissolution were also measured in natural populations during the PeECE III mesocosm study under differing ambient pCO₂ concentrations. Microzooplankton grazing accounted for between 27 and 70% of the dynamic calcite stock being lost per day, with no measurable effect of CO₂ treatment. These measured calcite dissolution rates indicate that dissolution of calcite in the guts of microzooplankton and copepods can account for the calcite losses calculated for the global ocean using budget and model estimates.