Learning Management Systems provide teachers with many functionalities to offer materials to students, interact with them and manage their courses. Recognizing teachers’ instructing styles from their course designs would allow recommendations and best practices to be made. We propose a method that determines teaching style in an unsupervised way from the course structure and use patterns. We define a course classification approach based on deep learning and clustering. We first use an autoencoder to reduce the dimensionality of the input data, while extracting the most important characteristics; thus, we obtain a latent representation of the courses. We then apply clustering techniques to the latent data to group courses based on their use patterns. The results show that this technique improves the clustering performance while avoiding the manual data pre-processing work. Furthermore, the obtained model defines seven course typologies that are clearly related to different use patterns of Learning Management Systems.