This is one of the first books to provide a systematic study of the many stochastic models used in systems biology. The book shows how the mathematical models are used as technical tools for simulating biological processes and how the models lead to conceptual insights on the functioning of the cellular processing system. Examples cover the phage lambda genetic switch, eukaryotic gene expression, noise propagation in gene networks, and more. Most of the text should be accessible to scientists with basic knowledge in calculus and probability theory.