A self-organizing tree (S-TREE) has a self-organizing capability and better performance than previously reported tree-structured clustering. In the S-TREE algorithm, since a tree grows in greedy fashion, a pruning mechanism is necessary to reduce the effect of bad leaf nodes. Extra nodes are pruned when the tree reaches a predetermined maximum size (U ). U is problem-dependent and is therefore difficult to specify beforehand. Furthermore, since U gives the limit of tree growth and also prevents self-organizing of the tree, it may produce unnatural clustering. We are presenting a new pruning algorithm without U . In this paper, we present results showing the performance of the new pruning algorithm using samples generated from normal distributions. The results of computational experiments showed that the new pruning algorithm works well for clustering of those samples.