Ontology-based approach in exploratory analysis of textual data can significantly improve the qualityof the obtained results. On the other hand, the use of domain knowledge defined in the form ofontologies increases the time needed to prepare a model and makes required calculations morecomplex. The publication will discuss selected aspects of cluster analysis performed on documentsautomatically annotated using ontologies. It seems that methodological aspects of cluster analysisprocess, especially the way in which distances are determined, should depend on the structure of agiven ontology. Three cases involving the use of ontologies with linear, hierarchical and networkstructures will be discussed. The methodological aspects of ontology-based cluster analysis of textdocuments was used for analysis of projects’ descriptions related to the area of economics andregistered in the period 2019-2021. Only Horizon and Framework Program projects were included.