Approaches to formalization of medical guidelines can be divided into model-centric and document-centric. While model-centric approaches dominate in the development of clinical decision support applications, document-centric, mark-up-based formalization is suitable for application tasks requiring the 'literal' content of the document to be transferred into the formal model. Examples of such tasks are logical verification of the document or compliance analysis of health records. The quality and efficiency of document-centric formalization can be improved using a decomposition of the whole process into several explicit steps. We present a methodology and software tool supporting the step-by-step formalization process. The knowledge elements can be marked up in the source text, refined to a tree structure with increasing level of detail, rearranged into an XML knowledge base, and, finally, exported into the operational representation. User-definable transformation rules enable to automate a large part of the process. The approach is being tested in the domain of cardiology. For parts of the WHO/ISH Guidelines for Hypertension, the process has been carried out through all the stages, to the form of executable application, generated automatically from the XML knowledge base.