Abstract We describe systematic changes that have been made to the Czech morphological dictionary related to annotating new data within the project of Prague Dependency Treebank (PDT). We bring new solutions to several complicated morphological features that occur in Czech texts. We introduced two new parts of speech, namely foreign word and segment. We adopted new principles for morphological analysis of global and inflectional variants, homonymous lemmas, abbreviations and aggregates. The changes were initiated by the need of consistency between the data and the dictionary and of the dictionary itself.