Responsive loads and energy storage units can play an important role to provide an economic and reliable operation of future energy systems. In this article, a stochastic energy and reserve market clearing scheme is presented considering demand response programs and energy storage devices. The approach is proposed to deal with stochastic and non-dispatchable renewable sources with high levels of penetration in the energy system. A two-stage stochastic programming scheme is formulated where in the first stage the energy market is cleared according to the forecasted amount of wind generation and demands and in the second stage the real time market is solved according to the assumed scenarios. Both stages are formulated as mixed integer linear programming problems. The introduced stochastic day-ahead scheduling scheme also regards load forecasting errors and unit/line outages. In order to generate sufficient scenarios for wind generation and demand uncertainties, the scenario generation procedure is defined as an optimization problem which is solved by particle swarm optimization algorithm.