In this paper, we will describe some theoretical and practical issues raised during the construction of the Basque Dependency Treebank (BDT): the syntactic annotation of EPEC (Reference Corpus for the Processing of Basque). EPEC is a 300,000 word corpus of standard written Basque whose purpose is to be a training corpus for the development and improvement of several NLP (Natural Language Processing) tools for Basque. BDT will be the first corpus for the Basque language tagged at syntactic level. We will also present the dependency-based annotation hierarchy that we have established for the syntactic tagging. Decisions made during design of the annotation hierarchy are based on the description of Basque grammar made by Euskaltzaindia (Academy for the Basque Language). When describing dependency relations, we consider lexical units as syntactic heads. This will open up a way for us to work with semantics.