Chromosomes of the human malaria parasite Plasmodiumfalciparum contain long subtelomeric repeat sequences and little is known about them. In this study, we have cloned 10 fragments of the non-coding rep20 sequence from the genome of Plasmodium falciparum 3D7 and HB3 strains. Analysis of these fragments showed that they represent 4 different 3D7 fragments and 2 different HB3 ones. Blasting the sequence of these fragments to the PlasmoDB revealed a varying degree of identity to the released rep20 sequence. One of these fragments was found to contain 27 degenerate repeats and show the highest consistency with the rep20 consensus sequence. This fragment was. inserted into a plasmid construct containing the green fluorescence gene and a stably transfected plasmodium cell line was established. Our data show that this rep20 fragment enhances the establishment of drug-resistant parasite populations after transfection; however it restricts the expression of the green fluorescence transgene. These results attract attention to an in-depth study of the role that some rep20 sequences may play between the telomeres and the differentially expressed virulence-related genes.