The paper introduces a new annotation of discourse relations in the Prague Dependency Treebank (PDT), i.e. the annotation of the so called secondary connectives (mainly multiword phrases like the condition is, that is the reason why, to conclude, this means etc.). Firstly, the paper concentrates on theoretical introduction of these expressions (mainly with respect to primary connectives like and, but, or, too etc.) and tries to contribute to the description and definition of discourse connectives in general (both primary and secondary). Secondly, the paper demonstrates possibilities of annotations of secondary connectives in large corpora (like PDT). The paper describes general annotation principles for secondary connectives used in PDT for Czech and compares the results of this annotation with annotation of primary connectives in PDT. In this respect, the main aim of the paper is to introduce a new type of discourse annotation that could be adopted also by other languages.