We compared the clinical and radiological results of posterior atlantoaxial fixation surgery using transarticular screws to those using a polyaxial screw–rod system in 55 patients with symptomatic atlantoaxial instability. Patients underwent posterior C1–C2 fixation: 28 patients (group 1) underwent C1–C2 transarticular screw fixation and 27 patients (group 2) underwent C1 lateral mass–C2 pedicle screw fixation. Patients were followed-up for at least 24 months. The clinical and radiological results were evaluated in the early postoperative period and at 3, 6, 12 and 24 months after surgery. Long-term postoperative stability and bone fusion were examined. After surgery, 93% of patients in group 1 and 96% of patients in group 2 were free of neck pain. The solid fusion rates were 82% for group 1 patients and 96% for group 2 patients at 12 months ( p < 0.092). In group 1, three patients showed fibrous union. Four patients had hardware failure due to a screw malposition (one in group 1) and pseudoarthrodesis (two in group 1 and one in group 2). One patient in group 1 had cerebrospinal fluid leakage. One patient in group 2 had occipital neuralgia. One vertebral artery injury occurred during the screw placement in group 1 and another in group 2 during the muscle dissection. C1–C2 transarticular screw fixation and C1 lateral mass–C2 pedicle screw fixation both produced excellent results for stabilization of the atlantoaxial complex, but the radiological outcome tended to be superior in C1 lateral mass–C2 pedicle screw fixation.