Myelodysplastic syndrome (MDS), which is known to be a preleukemic state, is a heterogeneous entity characterized by ineffective hematopoiesis and dysplastic morphological features. Most MDS patients show erosive telomeric repeats (TTAGGG)(n), without up-regulation of telomerase activity, suggesting that telomere shortening may be linked to cellular senescence in MDS. We measured telomere length in samples from 13 MDS patients and 8 healthy volunteers, based on telomere signals of individual chromosomes, using digital images of metaphases after quantitative fluorescence in situ hybridization (Q-FISH) with peptide nucleic acid probes and compared the results with results obtained with the standard method of determining terminal restriction fragment (TRF) length. In healthy volunteers, we found a significant correlation between TRF length and telomere fluorescence signals detected by Q-FISH, and a relatively wide distribution of fluorescence telomere signals was demonstrated in every sample. In contrast, we found no linear correlation between TRF length and telomere fluorescence signals in MDS, and most MDS patients showed weak telomere fluorescence signals, corresponding to short telomeres, with a narrow range compared with normal subjects. TRF length represented telomere DNA in whole marrow cells, whereas telomere fluorescence signals by Q-FISH represented only marrow metaphases corresponding to MDS-derived cells. Metaphases from most MDS patients showed homogeneous telomere shortening, irrespective of the presence of cytogenetic abnormality. In contrast, marrow metaphases from normal individuals showed a relatively wide range of telomere signals in each metaphase, indicating that in MDS cells, telomere shortening mechanisms that normally exist might be dysregulated. Therefore, analysis of telomere distribution as well as average telomere length detected by Q-FISH might be useful to clarify the telomere dynamics of MDS cells.