In multiple sclerosis (MS), gait impairment is one of the most prominent symptoms. For a sensitive assessment of pathological gait patterns, a comprehensive analysis and processing of several gait analysis systems is necessary. The objective of this work was to determine the best diagnostic gait system (DIERS pedogait, GAITRite system, and Mobility Lab) using six machine learning algorithms for the differentiation between people with multiple sclerosis (pwMS) and healthy controls, between pwMS with and without fatigue and between pwMS with mild and moderate impairment. The data of the three gait systems were assessed on 54 pwMS and 38 healthy controls. Gaussian Naive Bayes, Decision Tree, k-Nearest Neighbor, and Support Vector Machines (SVM) with linear, radial basis function (rbf) and polynomial kernel were applied for the detection of subtle walking changes. The best performance for a healthy-sick classification was achieved on the DIERS data with a SVM rbf kernel (κ = 0.49 ± 0.11). For differentiating between pwMS with mild and moderate disability, the GAITRite data with the SVM linear kernel (κ = 0.61 ± 0.06) showed the best performance. This study demonstrates that machine learning methods are suitable for identifying pathologic gait patterns in early MS.