This study compares laboratory measurements of porosity and permeability between twenty-three whole-core samples and fifty-four 1-in. (25-mm) plugs drilled from the centers of the same samples. All samples are coarsely bioclastic carbonates from Miocene carbonate platforms of the Marion Plateau, offshore northeast Australia (1 limestone and 22 dolostones). Whole-core porosities tend to be slightly higher (average 1.4 porosity units) than plug porosities, probably reflecting a lower surface/volume ratio for the larger samples. Permeability differences between whole cores and plugs vary greatly from sample to sample, but whole-core permeability tends to be higher in cases where larger differences are observed. This tendency may reflect flow through optimal-flow networks that occupy a small proportion of the total rock volume and are therefore not included within most plugs. Previous studies suggest that increasing permeability with sample scale may be a general characteristic of heterogeneous porous media. The present results provide a quantitative basis for evaluating the necessity and advantages of using whole cores as opposed to plugs for petrophysical characterization of carbonate reservoirs.