We outline the issues and decisions involved in creating a Penn-style treebank of Middle Low German (MLG, 1200-1650), which will form part of the Corpus of Historical Low German (CHLG). The attestation for MLG is rich, but the syntax of the language remains relatively understudied. The development of a syntactically annotated corpus for the language will facilitate future studies with a strong empirical basis, building on recent work which indicates that, syntactically, MLG occupies a position in its own right within West Germanic. In this paper, we describe the background for the corpus and the process by which texts were selected to be included. In particular, we focus on the decisions involved in the syntactic annotation of the corpus, specifically, the practical and linguistic reasons for adopting the Penn annotation scheme, the stages of the annotation process itself, and how we have adapted the Penn scheme for syntactic features specific to MLG. We also discuss the issue of data uncertainty, which is a major issue when building a corpus of an under-researched language stage like MLG, and some novel ways in which we capture this uncertainty in the annotation.