Twelve selected patients, eight males and four females aged 14 to 50 years, with syringomyelia associated with congenital craniovertebral bony anomalies including basilar invagination and fixed atlantoaxial dislocation, and associated Chiari I malformation in eight, were treated by atlantoaxial joint manipulation and restoration of the craniovertebral region alignment between October 2002 and March 2004. Three patients had a history of trauma prior to the onset of symptoms. Spastic quadriparesis and ataxia were the most prominent symptoms. The mean duration of symptoms was 11 months. The atlantoaxial dislocation and basilar invagination were reduced by manual distraction of the facets of the atlas and axis, stabilization by placement of bone graft and metal spacers within the joint, and direct atlantoaxial fixation using an inter-articular plate and screw method technique. Following surgery all patients showed symptomatic improvement and restoration of craniovertebral alignment during follow up from 3 to 20 months (mean 7 months). Radiological improvement of the syrinx could not be evaluated as stainless steel metal plates, screws, and spacers were used for fixation. Manipulation of the atlantoaxial joints and restoring the anatomical craniovertebral alignments in selected cases of syringomyelia leads to remarkable and sustained clinical recovery, and is probably the optimum surgical treatment.