In recent years, organs-on-chips (OOCs) have been developed to meet the desire for more realistic in vitro cell culture models. These systems introduce microfluidics, mechanical stretch and other physiological stimuli to in vitro models, thereby significantly enhancing their descriptive power. In most OOCs, porous polymeric membranes are used as substrates for cell culture. The polymeric material, morphology and shape of these membranes are often suboptimal, despite their importance for achieving ideal cell functionality such as cell–cell interaction and differentiation. The currently used membranes are flat and thus do not account for the shape and surface morphology of a tissue. Moreover, the polymers used for fabrication of these membranes often lack relevant characteristics, such as mechanical properties matching the tissue to be developed and/or cytocompatibility. Recently, innovative techniques have been reported for fabrication of porous membranes with suitable porosity, shape and surface morphology matching the requirements of OOCs. In this paper, we review the state of the art for developing these membranes and discuss their application in OOCs.