A game system includes a game apparatus and a controller. For example, whether an operation of waving the controller has been performed is determined based on at least one of a pointed position on a display screen by the controller and acceleration. A wind object is generated and moved in virtual game space according to the waving operation. When it is determined that the wind object has collided with a windmill object disposed in the virtual game space, the windmill object is influenced by the wind and its rotation speed is changed.