In a method of aligning wafers, a second wafer having at least one second alignment key may be arranged over a first wafer having at least one first alignment key. At least one alignment hole may be formed by passing through the second wafer to expose the second alignment key and the first alignment key. The first wafer and the second wafer may be aligned with each other using the first alignment key and the second alignment key exposed through the alignment hole. Thus, the first alignment key and the second alignment key exposed through the alignment hole may be positioned at a same vertical line to accurately align the first wafer with the second wafer.