The Design Optimisation of small energy Microgrids involves establishing the equipment configuration (size and capacity of components) and the operational rules for ongoing in service use. Existing techniques support the analysis of individual days of incident solar energy. In this paper a technique that uses Stochastic programming is proposed. The new technique allows the probability of occurrence of a particular day of incident solar energy, and the probability occurrence of particular consecutive days of incident solar energy to be considered by the optimisation process. The technique outlined supports the pre processing of incident solar energy and system loads as discrete probability functions which subsequently allows simple linear programming techniques to be utilised. This results in the ability to create easy to modify and easily scalable design tools.