Performing business process analysis in healthcare organizations is particularly difficult due to the highly dynamic,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 casestudy,but the same methodology can be used in other healthcare environments.