Chromosomal structure within the nucleus influences various biological processes such as transcription and replication. Telomeres are located at the end of eukaryotic chromosomes and they can be a decisive factor for correct chromosomal positioning. To gain new insight into telomere dynamics, we examined telomere length and positional changes during spermatogenesis using improved fluorescence in situ hybridization (FISH) and in situ telomeric repeat amplification protocols (TRAP) on histological sections. FISH revealed telomere length and chromosome position within nuclei change dynamically. Telomere extension occurred during spermiogenesis. In situ TRAP analysis verified elevated telomerase activity in elongating spermatids. Together, these data show that elongated spermatids have longer telomeres than precursor spermatogenic cells. This observation indicates that telomere elongation in haploid cells occurs after meiosis and in the absence of genomic replication. Analyses of testes from telomerase null mice further support the significance of telomere dynamics during spermatogenesis and the existence of an alternative telomere extension pathway.