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Background Chordoma is a rare malignant tumor of the axial skeleton. Percutaneous cryoablation (PCA) is a minimally invasive technique that allows freezing of tumors under imaging control. The purpose of our retrospective study was to investigate the outcome of PCA in a selected cohort of patients with sacrococcygeal chordoma, with a minimum of 5 years follow-up. Materials and methods Four patients were treated in 10 sessions. The mean follow-up was 57.3 months. We evaluated the feasibility, the procedure-related complications, the impact on pain control and oncological outcomes. Results Freezing of 100% of the tumor volume was possible in 60%. Pain control was not reliably evaluable. Local recurrence occurred in 90% of the treated lesions; the mean time to progression was 8.1 months (range 1.5-16). At last follow-up, one patient had died of the disease, one of another cause and one was receiving the best supportive care. The only patient alive without the disease had received additional carbon-ion radiotherapy. The 5-year survival rate after index PCA was 50%. Conclusion Complete freezing of the tumor was technically challenging, mainly due to the complex local anatomy. Recurrence occurred in 90% of the lesions treated. PCA should be considered with caution in the curative management of sacrococcygeal chordoma.