A game system includes a game apparatus and a controller. The controller is furnished with an acceleration sensor for detecting accelerations in at least two axis directions. Game processing corresponding to the kind of an acceleration input by means of the controller is executed. For determining the kind, reference timing when acceleration in a first-axis direction is below a threshold value to take on a minimum value is detected. Then, it is determined whether or not an angle between acceleration change vectors before and after the reference timing is equal to or more than a predetermined angle. When the angle is not equal to or more than the predetermined angle, it is determined that the acceleration input is an acceleration input in any one of the two-axis directions, and when the angle is equal to or more than the predetermined angle, it is determined that the acceleration input is an acceleration input in a direction including the two-axis directions as components.