Chromosome fragmentation (CF) constitutes one means of manipulating eukaryotic genomes and provides a powerful tool for examining both the structure and function of chromosomes. During the past 15 yr, CF, which is based on the use of transfection, has been widely used in yeast and mammals to elucidate the functional elements required for normal chromosome maintenance. However, in view of the relatively late development of parasite genome projects, this strategy has only been used recently in parasites. Here, we describe basic methods for CF (except telomere-mediated fragmentation) experiments and analysis in Leishmania. Current limitations of this methodology are precisely the lack of knowledge of the nature of centromeres and autonomously replicating sequences in this and other protozoa, the poor understanding of precise recombination mechanisms, as well as the fact that the deletion of unknown genes essential to parasite survival may interfere with recombination events and chromosomal rearrangements. Still, this powerful method has enriched our basic knowledge of chromosomal structure and maintenance.