Leishmania species are members of the evolutionarily ancient protozoan order Kinetoplastidae and are important human pathogens. The Leishmania genome is relatively small (∼34 Mbp) and is distributed among 36 chromosome pairs, ranging in size from 0.3 to 2.5 Mbp. The smallest chromosome of Leishmaniamajor Friedlin, chr1, consists of three homologues which differ in size by ∼29 kb. Previous sequence and Southern analyses of all three homologues reveal a conserved chromosomal core, consisting of coding and adjacent ‘non-informational’ sequence. Here we show the size difference between homologues is largely restricted to variation in both the number and content of several sub-telomeric repetitive elements localized on one chromosomal end. These repetitive elements also occur on other chromosomes, but some are more dispersed in the Leishmania genome than others.