The goal of the presented project is to assign a structure of clauses to Czech sentences from the Prague Dependency Treebank (PDT) as a new layer of syntactic annotation, a layer of clause structure. The annotation is based on the concept of segments, linguistically motivated and easily automatically detectable units. The task of the annotators is to identify relations among segments, especially relations of super/subordination, coordination, apposition and parenthesis. Then they identify individual clauses forming complex sentences. In the pilot phase of the annotation, 2,699 sentences from PDT were annotated with respect to their sentence structure.