In this paper a new stochastic-heuristic methodology for the optimisation of the electrical supply of stand-alone (off-grid) hybrid systems (photovoltaic-wind-diesel with battery storage) is shown. The objective is to minimise the net present cost of the system. The stochastic optimisation is developed by means of Monte Carlo simulation, which takes into account the uncertainties of irradiation, temperature, wind speed and load (correlated Gaussian random variables), using their probability density functions and the variance-covariance matrix. Also the uncertainty of diesel fuel price inflation rate was considered. The heuristic approach uses genetic algorithms to obtain the optimal system (or a solution near the optimal) in a reasonable computation time. This methodology includes an accurate weighted Ah-throughput battery model with several control variables, which can be set in the modern battery controllers or inverter/chargers with State of Charge control. A case study is analysed as an example of the application of this methodology, obtaining the stochastic optimisation an optimal system similar to the one obtained by the deterministic optimisation. It is recommended to perform first the deterministic optimisation (with low computation time), then the search space should be reduced and finally the stochastic optimisation can be obtained in a reasonable computation time.