The invention relates to an imaging apparatus, an imaging system, a method of controlling the apparatus and the system. An imaging apparatus includes a conversion unit including multiple pixels arranged in a matrix, each pixel including a conversion element, an output switch element, and an initialization switch element; an output drive circuit controlling an output operation; an initialization drive circuit controlling an initialization operation; a readout circuit performing a signal sample-and-hold operation and a reset operation; and a control unit performing the termination of the output operation of a certain row and the start of the output operation of another row after the reset operation is terminated, the start of the signal sample-and-hold operation after the output operation of the certain row is terminated and the output operation of the other row is started, the start of the reset operation and the initialization operation after the signal sample-and-hold operation is terminated, and the termination of the reset operation after the initialization operation is terminated.