This paper elaborates on the notion of uncertainty in the context of annotation in large text corpora, specifically focusing on (but not limited to) historical languages. Such uncertainty might be due to inherent properties of the language, for example, linguistic ambiguity and overlapping categories of linguistic description, but could also be caused by lacking annotation expertise. By examining annotation uncertainty in more detail, we identify the sources and deepen our understanding of the nature and different types of uncertainty encountered in daily annotation practice. Moreover, some practical implications of our theoretical findings are also discussed. Last but not least, this article can be seen as an attempt to reconcile the perspectives of the main scientific disciplines involved in corpus projects, linguistics and computer science, to develop a unified view and to highlight the potential synergies between these disciplines.