STOCHSIMGPU: parallel stochastic simulation for the systems biology toolbox 2 for Matlab. STOCHSIMGPU is a MATLAB plugin computing many realisations, so called ensemble, of stochastic simulations of chemical reaction systems in parallel on graphics processing units (GPUs). STOCHSIMGPU is tightly integrated into the Systems Biology Toolbox 2 for MATLAB and replaces its stochastic simulation code seamlessly. This means, you can benefit from using the computational power of your NVIDIA CUDA GPU without changing your model code. We present a new software tool STOCHSIMGPU which exploits GPUs for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made.