Background: Studies on the natural history of rare, chronic diseases like spinocerebellar ataxia 3 (SCA3) are hard to be done, since patients enter the study with variable disease durations and are followed up at irregular intervals. Aims: Our purpose was to use all the available data to describe the progression of gait ataxia in a long-term cohort of patients with SCA3 through a markovian method. Materials and Methods: SCA3 patients were recruited between 1998 and 2005 and were invited to annual neurological follow-ups until 2007. Gait ataxia was described through a mean score graph and a mean trajectory graph. Results: We followed up 105 patients; at baseline, the mean age and disease duration were, 40.5 (SD = 12.6) and 7.7 (SD = 5.8) years, respectively. The mean time to reach stages 1, 2, 3 and 4 of gait ataxia were 3, 5.4, 10.8 and 19.4 years of disease duration. The mean score graph was unsmooth, showing several unlikely ups and downs. The mean trajectory graph produced a continuous curve. Conclusion: The markovian method described the natural history of gait ataxia without any a posteriori adjustment of data and allowed statistical comparisons between subgroups. This method will be useful in future clinical trials in this and in other chronic degenerative diseases.