Development of balanced community of microorganisms is one of the obligatory for stable anaerobic digestion. Application of mathematical models might be helpful in development of reliable procedures during the process start-up period. Yet, the accuracy of forecast depends on the quality of input and parameters. In this study, the specific anaerobic activity (SAA) tests were applied in order to estimate microbial community structure. Obtained data was applied as input conditions for mathematical model of anaerobic digestion. The initial values of variables describing the amount of acetate and propionate utilizing microorganisms could be calculated on the basis of SAA results. The modelling based on those optimized variables could successfully reproduce the behavior of a real system during the continuous fermentation. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-NDlicense (http://creativecommons.org/licenses/by-nc-nd/3.0/).