A semiconductor device with a through via penetrating a semiconductor substrate, in which shorting between a wiring and a semiconductor element is prevented to improve the reliability of the semiconductor device. A liner insulating film as a low-k film, which has a function to insulate the semiconductor substrate and a through-silicon via from each other and is thick enough to reduce capacitance between the semiconductor substrate and the through-silicon via, is used as an interlayer insulating film for a first wiring layer over a contact layer. This prevents a decrease in the thickness of an interlayer insulating film in the contact layer.