Discourse structure and discourse relations are an important ingredient in systems for the analysis of text that go beyond the boundary of single clauses. Discourse relations often indicate important additional information about the connection between two clauses, such as causality, and are widely believed to have an influence on aspects of reference resolution.In this article, we first present the general design choices that are to be made in the design of an annotation scheme for discourse structure and discourse relations. In a second part, we present the scheme used in our annotation of selected articles from the TüBa-D/Z treebank of German (Telljohann et al., 2009). The scheme used in the annotation is theory-neutral, but informed by more detailed linguistic knowledge in the way of linguistic tests that can help disambiguate between several plausible relations.