The aim of this study is developing an automatic system for detection of gait-related health problems using Deep Neural Networks (DNNs). The proposed system takes a video of patients as the input and estimates their 3D body pose using a DNN based method. Our code is publicly available at https://github.com/rmehrizi/multi-view-pose-estimation. The resulting 3D body pose time series are then analyzed in a classifier, which classifies input gait videos into four different groups including Healthy, with Parkinsons disease, Post Stroke patient, and with orthopedic problems. The proposed system removes the requirement of complex and heavy equipment and large laboratory space, and makes the system practical for home use. Moreover, it does not need domain knowledge for feature engineering since it is capable of extracting semantic and high level features from the input data. The experimental results showed the classification accuracy of 56% to 96% for different groups. Furthermore, only 1 out of 25 healthy subjects were misclassified (False positive), and only 1 out of 70 patients were classified as a healthy subject (False negative). This study presents a starting point toward a powerful tool for automatic classification of gait disorders and can be used as a basis for future applications of Deep Learning in clinical gait analysis. Since the system uses digital cameras as the only required equipment, it can be employed in domestic environment of patients and elderly people for consistent gait monitoring and early detection of gait alterations.