C(2) pedicle screw is the classic instrumentation for posterior C(2) fixation. But it could be dangerous in case of anatomical variation, such as high riding vertebral artery and small C(2) pedicle. C(2) trans-laminar screw could be an alternative choice. This retrospective study is to evaluate the feasibility of C(2) trans-laminar screw for atlantoaxial instability with anatomical variation. In our clinical work, we had nine atlantoaxial instability cases with C(2) pedicle malformation. If the malformation is unilateral, we inserted one C(2) trans-laminar screw and one C(2) pedicle screw in the normal pedicle; if the malformation is bilateral, bilateral trans-laminar screws were used. Then C(2) instrumentation could be connected with C(1) lateral mass screw or occipital screw in cases with C(1) occipitalization. Then atlantoaxial or occipitocervical fusion could be done with morselized autogenous cancellous iliac grafts. Nine cases had C(2) trans-laminar screw, including 2 atlantoaxial fusion and 7 occipitocervical fusion. Six cases had unilateral trans-laminar screw and 3 had bilateral trans-laminar screw. Radiographs demonstrated all the screws were placed satisfactorily except one. There was no neurological deterioration or vertebral artery injury. All the cases had an average follow-up of 9 months (4 - 13 months). All patients attained solid fusion without screw failure. In the 8 cases with neurological deficit, 3 were excellent, 1 was good, 2 were fair and 2 had no change. C(2) trans-laminar screw fixation could provide sufficient stability. This technique could be an alternative to standard C(2) pedicle screw in cases with pedicle malformation and high riding vertebral artery. It is safe and simple in experienced hands.