Aims: To evaluate whether the atlantoaxial disorders (anterior atlantoaxial subluxation and atlantoaxial impaction) associate with destruction of shoulder or peripheral joints, and bone mineral density (BMD) in patients with long-term rheumatoid arthritis (RA). Methods: An inception cohort 67 patients with seropositive and erosive RA were followed up for 20 years. Cervical spine, shoulder, hand and foot radiographs, and the BMD of the lumbar spine and femoral neck were evaluated. Results: A positive relationship was detected between the occurrence of atlantoaxial disorders and the destruction of both shoulder (p < 0.001) and peripheral (p = 0.001) joints. In addition, the severity of atlantoaxial disorders positively correlated with the grade of destruction in the evaluated joints. Furthermore, a positive relationship was found between the occurrence of the atlantoaxial disorders and a decrease in BMD of the femoral neck (p = 0.019). Conclusions: Patients with severe RA and osteoporosis have an increased risk for atlantoaxial disorders, therefore the cervical spine radiographs of these patients should be analysed before major surgery and also at regular intervals. The co-existence of shoulder and cervical spine disorders makes the differential diagnosis of shoulder and neck pain challenging.