We developed the biochemical reaction simulator called WinBEST-KIT (Biochemical Engineering System analyzing Tool-KIT, which runs under Microsoft Windows) for analyzing complicated biochemical reaction systems such as metabolic pathways. WinBEST-KIT provides an integrated simulation environment for experimental researchers. A particularly notable feature is that users can define the original mathematical equations representing unknown kinetic mechanisms and customize them as the reaction steps of GUI components. We believe that WinBEST-KIT will become one of the most efficient biochemical reaction simulators for experimental researchers.