The development of Internet resulted in an increasing number of online text re-positories. In many cases, documents are assigned to more than one class and automatic multi-label classification needs to be used. When the number of labels exceeds the number of the documents, effective label space dimension reduction may signifi-cantly improve classification accuracy, what is a major priority in the medical field. In the paper, we propose document clustering for label selection. We use semi-clustering method, by considering graph representation, where documents are represented by vertices and edge weights are calculated according to their mutual similarity. Assigning documents to semi-clusters helps in reducing number of labels, further used in multilabel classification process. The performance of the method is examined by experiments conducted on real medical datasets.