A method for fabricating a metal-oxide semiconductor (MOS) transistor. A substrate having a gate structure is provided. The method of the invention includes forming a liner spacer on each side of the gate structure and a low dopant density region deep inside the substrate. The low dopant density region has a lower dopant density than that of a lightly doped region of the MOS transistor. Then a interchangeable source/drain region with a lightly doped drain (LDD) structure and an anti-punch-through region is formed on each side of the gate structure in the low dopant density region. The depth of the interchangeable source/drain region is not necessary to be shallow.