A cell culture container includes, in sequence from above in the gravity direction: a culture-medium holding container; a cell holding container that holds cells and a culture medium supplied from the culture-medium holding container through a supply port provided in the top surface thereof; a waste-liquid holding container that holds the culture medium discharged from the cell holding container; and a discharge mechanism for discharging the culture medium that has exceeded a predetermined level from the cell holding container to the waste-liquid holding container.