Abstract A case study based on experience in linguistic investigations using annotated monolingual and multilingual text corpora; the “cases” include a description of language phenomena belonging to different layers of the language system: morphology, surface and underlying syntax, and discourse. The analysis is based on a complex annotation of syntax, semantic functions, information structure and discourse relations of the Prague Dependency Treebank, a collection of annotated Czech texts. We want to demonstrate that annotation of corpus is not a self-contained goal: in order to be consistent, it should be based on some linguistic theory, and, at the same time, it should serve as a test bed for the given linguistic theory in particular and for linguistic research in general.