Biological systems are inherently stochastic, a fact which is often ignored when simulating genetic circuits. Synthetic biology aims to design genetic circuits de novo, and cannot therefore afford to ignore the effects of stochastic behavior. Since computational design tools will be essential for large-scale synthetic biology, it is important to develop an understanding of the role of stochasticity in molecular biology, and incorporate this understanding into computational tools for genetic circuit design. We report upon an investigation into the combination of evolutionary algorithms and stochastic simulation for genetic circuit design, to design regulatory systems based on the Bacillus subtilis sin operon.