Background Dystonia is a ubiquitous syndrome, with a growing number of genes being continually identified. Mutations in the anoctamin-3 gene have been described to cause dystonia but the management and long-term outcomes are still largely unknown. Methods We present here a long term, longitudinal follow up of a patient with generalized dystonia, who was treated with bilateral pallidal deep brain stimulation and was found to harbor a mutation in the anoctamin-3 gene. Results Ongoing adjustment of stimulation settings and medications led to good and sustained dystonia control; however the patient did suffer short term relapses, manifested as dystonic crisis, which necessitated inpatient admission. Conclusion This only the second patient to be reported with pallidal stimulation and an anoctamin-3 gene mutation. Long term outcomes seem to be favorable but larger case series are needed to confirm our findings.