Spinocerebellar ataxia 3 is an untreatable CAG repeat expansion disorder whose natural history is not completely understood. Our aims were to describe the progression of neurological manifestations in a long-term cohort of spinocerebellar ataxia 3, and to verify if CAG expanded repeat, gender, and age at onset were associated with the rate of progression. Patients entered the study between 1998 and 2005 and were seen until 2007. On each visit, the validated NESSCA scale, an inventory of 18 neurological manifestations, was applied. Scores observed in each year of disease duration produced a Growth Curve, which was analyzed through the random coefficients model. Scores obtained in some individual items were described through multi-state Markov models. One hundred fifty-six patients (78 families) were recruited; 28 were lost, and 23 died. Mean (sd) ages at onset and at baseline were 32.8 (10.6) and 40.7 (12.8) years; median (range) expanded CAGn was 74 (67–85). Three hundred fifteen NESSCA evaluations were performed, comprising disease durations from zero to 34 years. The 105 patients who completed the study were seen over 5 (sd = 2.4) years at intervals of 2.5 (sd = 1.5) years. The trajectory of NESSCA obtained for the overall group increased by 1.26 points per year. This slope increased by 0.15 points per each additional CAG in the expanded repeat ( p  < 0.0002) and decreased by 0.03 points per each additional year of age at onset ( p  = 0.005). NESSCA worsened steadily, producing linear trajectories, which were faster among patients with longer expanded repeats (>74) and with lower ages at onset (<34 years).