The annotation of the Prague Dependency Treebank (PDT) is conceived of as a multilayered scenario that comprises also dependency representations (tectogrammatical tree structures, TGTS’s) of the underlying structure of the sentences. TGTS’s capture three basic aspects of the underlying structure of sentences: (a) the dependency tree structure, (b) the kinds of dependency syntactic relations, and (c) the basic characteristics of the topic-focus articulation (TFA). Since the PDT is a large collection and the annotations on the deepest layer are to a large extent performed by several human annotators (based on an automatic preprocessing module), it is more than necessary to observe the consistence of annotators and the agreement among them. In the present paper, we summarize the results of the evaluation of parallel annotations of several samples taken from PDT and the measures accepted to improve the consistency of annotations.