ModeRator is an online software tool for comparison of stoichiometric models written in COBRA-compatible format. Its main purpose is to detect the inconsistencies of complex models and to compare the models even without having Matlab and COBRA toolbox installed on a computer. The tool can be used online at http://biosystems.lv/moderator/ or hosted on a local computer. ModeRator is implemented in pure PHP, and its source code can be downloaded from http://sourceforge.net. The application and installation instructions are available. Additionally, a video tutorial is available on Youlube. ModeRator was tested on two representative genome-scale metabolic network models of Zymomonas Mobilis. The results show that the proposed software tool is able to correctly analyse/compare the models.