BACKGROUND: Telomeres are specialized nucleoprotein structures at chromosome ends that undergo dynamic changes after each cell cycle. Understanding the mechanisms of telomere dynamics is critically dependent on the ability to accurately measure telomere length in a cell population of interest. Techniques such as Southern blot, which measures average telomere length, and quantitative fluorescence in situ hybridization (Q-FISH), which can estimate telomere length in individual chromosomes, are limited in their capacity to determine the distribution of cells with differing telomere lengths in a given cell population. METHODS: We employed flow-FISH to determine whether mouse and human cell lines exhibit subpopulations of cells with differing telomere lengths. RESULTS: Our analysis showed that at least one of four analyzed mouse cell lines had two subpopulations of cells with differing telomere lengths. Differences in telomere length between subpopulations of cells were significant, and we term this phenomenon TELEFLUCS (TElomere LEngth FLUctuations in Cell Subpopulations). We also observed TELEFLUCS in 1 of 19 analyzed human nonalternative lengthening of telomere cell lines and in 1 of 2 analyzed human alternative lengthening of telomere cell lines. The existence of cell subpopulations with differing telomere lengths was confirmed by Q-FISH. CONCLUSION: Our results underscore the importance of flow-FISH in telomere length analysis. 2004 Wiley-Liss, Inc.