Experimental investigations were carried out in order to evaluate the substrate permeability of starch and its microbial metabolites, using the pellets of Aspergillus niger formed by 5-d culture. The distribution coefficients were almost constant irrespective of the initial total organic carbon (TOC) concentration, but decreased slightly with increase in the pellet diameter. This trend was negligible for substrates other than soluble starch and their average distribution coefficients were almost unity. The apparent intra-pellet diffusion coefficients of these substrates and oxygen increased with increase in the pellet diameter, and were almost identical for the same diameter of pellet regardless of the substrate. It was suggested that mass transfer flow rate of substrate appeared to be higher because of a sparser structure and a lower density with larger diameter of pellets formed by 5-d culture.