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Purpose To investigate dose distribution variations due to setup errors and range uncertainties in image-guided carbon ion radiotherapy of head chordoma. Materials and methods Ten treatment plans were retrospectively tested with TRiP98 against ±1.0mm and ±1.0° setup errors, as observed in clinical routine, and 2.6% range uncertainty when 2mm CTV-to-PTV margins were applied. Single-fraction simulations were compared with the total treatment dose in terms of DVH bands, conformity and inhomogeneity. The contribution of image processing artifacts on reported results was also discussed, as a function of the imaging dataset resolution. Results Results showed that safety margins grant the conformal target coverage in presence of setup errors with D95 CTV variations below 10% in 7 patients out of 10. Instead, the inclusion of range uncertainty yielded to appreciable dose degradation, reporting larger effects for CTV and dose conformity, whereas reduced impact is found on the organ-at-risk. The fractionation scheme positively affects dose conformity and inhomogeneity; conversely its influence on DVH bands is strongly related to the patient anatomy. Conclusion Besides safety margins, setup and range uncertainties lead to non-negligible combined contribution. Systematical treatment plan robustness assessment against expected uncertainties is thus encouraged, selecting beam settings and fractionation schemes where homogeneity is preserved.