Thanks to the explosion of heterogeneous healthcare data and advanced machine learning and data mining techniques, specifically deep learning methods, we now have an opportunity to make difference in healthcare. In this tutorial, we will present state-of-the-art deep learning methods and their real-world applications, specifically focusing on exploring the unique characteristics of different types of healthcare data. The first half will be spent on introducing recent advances in mining structured healthcare data, including computational phenotyping, disease early detection/risk prediction and treatment recommendation. In the second half, we will focus on challenges specific to the unstructured healthcare data, and introduce advanced deep learning methods in automated ICD coding, understandable medical language translation, clinical trial mining, and medical report generation. This tutorial is intended for students, engineers and researchers who are interested in applying deep learning methods to healthcare, and prerequisite knowledge will be minimal. The tutorial will be concluded with open problems and a Q&A session.