The benthic body size miniaturization hypothesis states that deep-sea communities are dominated by organisms of smaller body size, although some field studies have produced contradictory results. Using appropriate sample sets, this study tests this hypothesis by contrasting the benthic communities of the Fladen Ground (North Sea, 150 m) and the Faroe–Shetland Channel (1600 m). Samples were collected for large (500 μm) and small macrofauna (250–355 μm), meiofauna (45 μm) as well as an intermediate sized ‘mesofauna’ (180 μm) to ensure comprehensive coverage of the full meio- and macro-faunal body size-range. The body size structure of the benthos was compared using two methods. The more widely used average individual biomass method involves dividing the total sample biomass by sample abundance. Additionally, body size accumulation curves were constructed by assigning all specimens into a logarithmic size-class and then plotting the cumulative percentage of individuals present in each size-class. The results seem to support the hypothesis that the deep-sea environment is a small organism habitat. Although these findings only represent two locations, the overall body size accumulation curves clearly display a statistically significant shift towards smaller body sizes at the deeper site. The magnitude of the effect is appreciable with median metazoan body size reducing from 14.3 μg wet weight in the Fladen Ground to 3.8 μg wet weight in the Faroe–Shetland Channel. The average individual biomass measurements are shown to be of limited value and can lead to potentially misleading conclusions if the underlying size structure is not analysed in detail.