Abstract: Neurodegenerative diseases affect a large part of the population in the world and also in Mexico, deteriorating gradually the quality of patients’ life. Therefore, it is important to diagnose them with a high degree of reliability. In order to solve it, various computational methods have been applied in the analysis of biomarkers of human gait. In this study, we propose employing the automatic model selection and hyperparameter optimization method that has not been addressed before for this problem. Our results showed highly competitive percentages of correctly classified instances when discriminating binary and multiclass sets of neurodegenerative diseases: Parkinson’s disease, Huntington’s disease, and Spinocerebellar ataxias.