The creation of tools supporting the automatization of the standardization and continuous control of healthcare processes can become a significant helping tool for clinical experts and healthcare systems willing to reduce variability in clinical practice. The reduction in the complexity of design and deployment of standard Clinical Pathways can enhance the possibilities for effective usage of computer assisted guidance systems for professionals and assure the quality of the provided care. Several technologies have been used in the past for trying to support these activities but they have not been able to generate the disruptive change required to foster the general adoption of standardization in this domain due to the high volume of work, resources, and knowledge required to adequately create practical protocols that can be used in practice. This chapter proposes the use of the PALIA algorithm, based in Activity-Based process mining techniques, as a new technology to infer the actual processes from the real execution logs to be used in the design and quality control of healthcare processes.