Rationale: Atlantoaxial subluxation (AAS), caused by congenital factors, inflammation such as rheumatoid arthritis, infection, neoplasia, or trauma, is rare and severely erodes and subluxates atlantoaxial (AA) joints. For these patients, surgical reduction, and stabilization are difficult. Surgery, including anterior transoral decompression and posterior fixation, anterior endonasal decompression and fixation, and posterior decompression with AA or occipitocervical fixation, is often the only treatment available. However, there have only been 2 reports of C1-C2 facet spacer use in treating AAS. Here, we report the case histories of 3 patients with severely damaged and subluxated AA joints and symptomatic basilar invagination (BI), malalignment, or C2 root compression. Patient concerns: The cases included 2 women with rheumatoid arthritis and 1 man with spondyloarthropathy secondary to ulcerative colitis. Diagnosis: Radiographic imaging revealed severely damaged and subluxated AA joints. Their symptoms included worsening pain in the neck or occiput with or without myelopathy and neuralgia. Interventions: After realignment with C1-C2 spacers and posterior C1-C2 screw fixation, the patient symptoms were resolved. Outcomes: Of note, 2 of the 3 patients were healed without complications. One patient who underwent secondary revision surgery because of rod breakage and obvious nonunion at C0-C2 was determined to be healed at 1-year follow-up after the revision surgery. Lessons: We confirmed that C1-C2 facet spacers both reduced BI and occipitocervical coronal malalignment as well as releasing C2 root compression. Therefore, surgical restoration and fixation should be a required treatment in this very rare group of patients.