Clustering XML documents according to their structure is one of the techniques that may improve the effectiveness of XML documents storage and retrieval. One of existing approaches to this problem is to encode XML document structure as a string of bits and cluster such feature vectors. High dimensionality and sparseness of the feature vectors are the weaknesses of this method. The paper presents four methods reducing the dimensionality of the bit feature vectors. Two of these methods are novel. They are dedicated to XML documents and should be applied during the encoding process. The results showed good efficiency of these inner-encoding methods and their ability of improving clustering results in some cases. The methods presented in the paper are tested on two datasets of XML documents having different characteristics.