Studies were made to determine the effect of the phase equilibrium on the mass balances and, thus, on the estimation of kinetic parameters in a batch reactor. The hydrotreating reactions of two model compounds, phenol and thiophenol, were used as test reactions. Losses in the molar balance of aromatic compounds were relatively large when calculation was based solely on the analysis of the liquid samples. To compensate for the lack of quantitative analysis of the gas phase, the gas composition in equilibrium with the analyzed liquid phase under the reaction conditions was simulated. In this way, the molar balances were improved to the level of accuracy needed for the estimation of kinetic parameters. With thiophenol, the accuracy limit was reached at conversions up to 85%. With phenol, the improvement of the mass balances was confused due to coking reactions which were remarkable already at low conversions. However, the simulation clearly increased the precision of the parameters. The routes to the less volatile reaction products were overweighted when data from the liquid phase analysis only were used in the estimation of kinetic parameters.