Syntactic annotation of historical text, with no access to native-speaker intuitions, poses a number of problems to the annotator who is faced with the task of giving a single analysis of each sentence. This article reports on the experiences from annotating complementation structures in Old Church Slavonic and Old East Slavonic in the PROIEL and TOROT treebanks. Two case studies are examined: complement clauses in Old Church Slavonic and the history of Russian čьto ‘what, which, that’. In the first case the annotation scheme is shown to work well in terms of interannotator agreement and retrievability. However, the price is that a large number of examples with jako ‘that’ are analysed as complement clauses with a subjunction, even though many of these examples are in fact ambiguous and jako can equally well be interpreted as a quotative particle followed by direct speech. The second case study looks at a development from situation where čьto could be taken to be an interrogative pronoun in all subordinated clauses, to a situation where a subjunction and a relative pronoun analysis are also available. This leads to a large number of ambiguous occurrences. The solution in TOROT is to analyse unambiguous interrogative pronoun and subjunction examples at face value, while all of the remaining occurrences are analysed as relative clauses. This makes the annotator’s job manageable, but causes retrievability problems, since individual researchers will have to sift through the relative clause examples themselves.