Three types of references occur in the annotation of PDT 2.0: references within one layer (e.g. between nodes of a tectogrammatical tree), references to objects (nodes or elements) of lower layers, and references to other sources (valency lexicon). All these references are realized in the same manner as described below.

The referred object is assigned an identifying attribute the value of which functions as an unique identifier of the object within PDT 2.0. The reference itself is realized by an attribute (atomic attribute of the type reference) containing the unique identifier of the referred object. If the referred object does not belong to the same file as the referring object, the identifier reference is prefixed with a prefix symbolic#, in which symbolic is a symbolic name associated with the filename containing the referred object. The association between symbolic names and filenames is to be found in the header of the referring file. This mapping is unambiguous and file-specific.

By a convention, in PDT 2.0, the names of all attributes containing references or lists of references bear the suffix .rf. Attributes carrying unique identifiers are usually named id (however, there are exceptions e.g. in the PDT Valency Lexicon vallex.xml the identifiers are contained in attributes word_ID and frame_ID for historical reasons).