To evaluate the musculoskeletal and soft tissue neural alterations in cases with group A basilar invagination . Between January 2007 and August 2016, 510 patients with group A basilar invagination were surgically treated. The radiologic images of these patients were reviewed retrospectively. The patients were divided into 4 groups: group A1, comprising 60 patients with syringomyelia ; group A2, comprising 354 patients with “external syrinx,” marked by excessive cerebrospinal fluid (CSF) in the extramedullary space; group A3, comprising 51 patients with both syringomyelia and external syrinx; and group A4, comprising 45 patients with no abnormality of CSF cavitation in the spinal canal. A number of musculoskeletal and neural parameters, including the extent of basilar invagination, degree of angulation of the odontoid process , and facet malalignment, were evaluated in each of the 4 groups. The degree of basilar invagination was 6–27.4 mm (average, 15.85 mm) in group A1, 4.3–24.5 mm (average, 12.56 mm) in group A2, 5.6–17.6 mm (average 10.8 mm) in group A3, and 5.2–17.3 mm (average, 11.74 mm) in group A4. The angle of inclination of the odontoid process was 61.1–90.7 degrees (average, 71.4 degrees) in group A1, 30.5–79.8 degrees (average, 60.05 degrees) in group A2, 68.5–78.3 degrees (average, 73.4 degrees) in group A3, and 62.2–87.4 degrees (average, 71.2 degrees) in group A4. The nature of bone malformations directly influences the presence or absence of external syrinx and syringomyelia.