Ataxic gait monitoring and assessment of neurological disorders belong to important multidisciplinary areas that are supported by digital signal processing methods and machine learning tools. This paper presents the possibility of using accelerometric data to optimise deep learning convolutional neural network systems to distinguish between ataxic and normal gait. The experimental dataset includes 860 signal segments of 16 ataxic patients and 19 individuals from the control set with the mean age of 38.6 and 39.6 years, respectively. The proposed methodology is based upon the analysis of frequency components of accelerometric signals simultaneously recorded at specific body positions with a sampling frequency of 60 Hz. The deep learning system uses all of the frequency components in a range of 〈0,30 〉 Hz. Our classification results are compared with those obtained by standard methods, which include the support vector machine, Bayesian methods, and the two-layer neural network with features estimated as the relative power in selected frequency bands. Our results show that the appropriate selection of sensor positions can increase the accuracy from 81.2% for the foot position to 91.7% for the spine position. Combining the input data and the deep learning methodology with five layers increased the accuracy to 95.8%. Our methodology suggests that artificial intelligence methods and deep learning are efficient methods in the assessment of motion disorders and they have a wide range of further applications.