A semiconductor device includes a first structure including a first bonding structure, and a second structure on the first structure and including a second bonding structure connected to the first bonding structure. The first bonding structure includes a first insulating layer, a first bonding insulating layer on the first insulating layer, first bonding pads penetrating at least a portion of the first insulating layer and the first bonding insulating layer, and first metal patterns in the first insulating layer and in contact with the first bonding insulating layer, and having an upper surface at a lower level than upper surfaces of the first bonding pads. The second bonding structure includes a second bonding insulating layer bonded to the first bonding insulating layer, a second insulating layer on the second bonding insulating layer, and second bonding pads penetrating the second bonding insulating layer and connected to the first bonding pads.