Electronic Medical Records (EMR) contain a lot of valuable data about patients, which is however unstructured. There is a lack of labeled medical text data in Russian and there are no tools for automatic annotation. We present an unsupervised approach to medical data annotation. Morphological and syntactical analyses of initial sentences produce syntactic trees, from which similar subtrees are then grouped by Word2Vec and labeled using dictionaries and Wikidata categories. This method can be used to automatically label EMRs in Russian and proposed methodology can be applied to other languages, which lack resources for automatic labeling and domain vocabularies.