Gene network analysis is complicated by fluctuations associated with discrete reaction events in small-number reactant pools. Although deterministic models are often used with success, there are many examples for which deterministic descriptions fail to capture essential features of the underlying stochastic system. We will discuss how genetic circuit models are formulated mathematically from biological principles, leading to deterministic systems of differential equations. We will then focus on the role of molecular noise in circuit function and ask how the full stochastic problem may be formulated.