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The paper deals with the problem of an analysis of complex sentences in Czech on the basis of manually annotated data. The availability of a specialized corpus explicitly describing mutual relationships between segments and clauses in Czech complex sentences, together with the availability of a thoroughly syntactically annotated corpus, the Prague Dependency Treebank, provide a solid background for linguistic investigation. The paper presents quantitative, linguistic and structural observations which provide a number of clues for building an algorithm for analyzing a structure of complex sentences in the future.