Methods of manufacturing an integrated circuit device including a through via structure are provided. The methods may include forming an isolation trench through a substrate to form an inner substrate, which is enclosed by the isolation trench and forming an insulating layer in the isolation trench and on a surface of the substrate. The methods may also include forming a hole, which is spaced apart from the isolation trench and passes through a portion of the insulating layer formed on the surface of the substrate and the inner substrate and forming a conductive layer in the hole and on the insulating layer formed on the surface of the substrate. The methods may be used to manufacture image sensors.