Performing business process analysis in healthcare organizations is particularly difficult due to the highlydynamic, complex, ad-hoc, and multi-disciplinary nature of healthcare processes. Process mining is a promising approach to obtain a better understanding about those processes by analyzing event data recorded in healthcare information systems. However, not all process mining techniques perform well in capturing the complex and ad-hoc nature of clinical workflows. In this work we introduce a methodology for the application of process mining techniques that leads to the identification of regular behavior, process variants, and exceptional medical cases. The approach is demonstrated in a case study conducted at a hospital emergency service. For this purpose, we implemented the methodology in a tool that integrates the main stages of process analysis. The tool is specific to the case study, but the same methodology can be used in other healthcare environments.