A game system comprising: a game controller; and a main body apparatus, the game controller having a first operation portion, a second operation portion, a first transmission unit (101, sq4) configured for transmitting, while connection with the main body apparatus has not been established, to the main body apparatus a connection signal in accordance with at least any of an operation onto the first operation portion and an operation onto the second operation portion, and a storage unit configured for storing a first operation time at which the operation onto the first operation portion has been performed and a second operation time at which the operation onto the second operation portion has been performed while connection with the main body apparatus has not been established, the main body apparatus having a connection unit configured for performing processing for establishing connection with the game controller in accordance with the connection signal, and a second transmission unit configured for transmitting to the game controller, a request signal requesting for information on the operation time stored in the storage unit when the processing for establishing connection is completed, the game controller further having a third transmission unit (101, sq32) configured for transmitting the information on the operation time stored in the storage unit to the main body apparatus in response to the request signal, and the main body apparatus further having a determination unit configured for determining whether the operation onto the first operation portion and the operation onto the second operation portion satisfy a predetermined condition based on the information on the operation time, a registration unit configured for registering a first operation scheme as an operation scheme of the game controller when a result of determination by the determination unit is affirmative, wherein the first operation scheme is a scheme of vertically holding the controller or laterally holding the controller; and a game processing execution unit configured for performing game processing based on at least any of a first operation signal in accordance with the operation onto the first operation portion and a second operation signal in accordance with the operation onto the second operation portion. a game controller; and a main body apparatus, the game controller having a first operation portion, a second operation portion, a first transmission unit (101, sq4) configured for transmitting, while connection with the main body apparatus has not been established, to the main body apparatus a connection signal in accordance with at least any of an operation onto the first operation portion and an operation onto the second operation portion, and a storage unit configured for storing a first operation time at which the operation onto the first operation portion has been performed and a second operation time at which the operation onto the second operation portion has been performed while connection with the main body apparatus has not been established, the main body apparatus having a connection unit configured for performing processing for establishing connection with the game controller in accordance with the connection signal, and a second transmission unit configured for transmitting to the game controller, a request signal requesting for information on the operation time stored in the storage unit when the processing for establishing connection is completed, the game controller further having a third transmission unit (101, sq32) configured for transmitting the information on the operation time stored in the storage unit to the main body apparatus in response to the request signal, and the main body apparatus further having a determination unit configured for determining whether the operation onto the first operation portion and the operation onto the second operation portion satisfy a predetermined condition based on the information on the operation time, a registration unit configured for registering a first operation scheme as an operation scheme of the game controller when a result of determination by the determination unit is affirmative, wherein the first operation scheme is a scheme of vertically holding the controller or laterally holding the controller; and