In this paper, we present that the result of document clustering can change dramatically with respect to the different ways of indexing compound nouns. First of all, the automatic indexing engine specialized for Korean words analysis, which also serves as the backbone engine for automatic document clustering system, is introduced. Then, the details of hierarchical agglomerative clustering(HAC) method, one of the widely used clustering methodologies in these days, was illustrated. As the result of observing the experiments, carried out in the final part of this paper, it comes to the conclusion that the various modes of indexing compound nouns have an effect on the outcome of HAC.