Clustering techniques are widely used to give insight about the similarities/dissimilarities between data set items. Most algorithms require the user to tune parameters such as number of clusters or threshold for cut-off point in a dendrogram. Such parameters also affect the clustering quality. In a good quality cluster, the intra-cluster similarity should be high, whereas the inter-cluster similarity should be low. To determine the optimal cluster number, several cluster validity methods have been proposed. However, there is no guideline with respect to which clustering validity methods can be used in conjunction with which clustering algorithms. In this paper, Dunn and SD validity indices were applied to Kohonen self organizing maps, k-means and agglomerative clustering algorithms and their limitations were shown empirically.