A capsule endoscope system includes a capsule endoscope and a receiver. The capsule endoscope has plural image pickup units for endoscopic imaging by passing a gastrointestinal tract in a body. The receiver for wireless communication with the capsule endoscope receives and stores image data from the capsule endoscope. The receiver includes a data analyzer for retrieving position relationship data expressing a position relationship of the image pickup units to a target region in the gastrointestinal tract. A CPU of the receiver produces a command signal according to the position relationship data for determining a number of frames of imaging per unit time for respectively the plural image pickup units. The capsule endoscope includes a CPU for controlling operation of the plural image pickup units according to the command signal from the receiver.
