Deposit-feeders are common components of macrofaunal assemblages in intertidal soft sediments. Predation has been considered to have a central role in affecting their distribution and population dynamics. This study investigates the effect of epibenthic predators on deposit-feeders, inhabiting the shallow layers of the sediment (surface and subsurface) and also the deepest layers (e.g., burrowing shrimp Upogebia pusilla; Petagna). The experiment was conducted in summer 2000 (August–September) at three different sites on an intertidal flat in Mediterranean Sea. In the field, predators were excluded using cages, placed on the surface of the sediment. It was predicted that under the cages, (i) abundances of animals would increase and (ii) species composition of assemblages would change as an effect of the exclusion of predators. Potential artefacts caused by the cages were controlled using partial cages (PC). Composition of organic matter and porosity were also analysed under PC and in natural controls to test whether the presence of cages would change sediment characteristics on the surface. At the end of the experiment, there were no significant differences in the composition of organic matter between PC and the undisturbed sediment (UC). After 8 weeks from the beginning of the experiment, exclusion of predators enhanced the abundance of U. pusilla. There were, however, no clear-cut changes in the species composition of macrofaunal assemblages and densities of animals did not increase under the cages. Indeed, some animals (Oligochaeta, Brania oculata, and Tanais dulongii) were less abundant under the cages (EC) than outside (PC and UC). We propose that predation might play a role in regulating interspecific relationships among some surface deposit-feeders and the burrowing shrimp U. pusilla.