Malaria affects millions of individuals, with an annual death toll of 200 000, mostly among children under 5 years of age according to WHO report 2014. Malaria is a vector borne disease that is able to evade the immune system through a very sophisticated surface antigen strategy, which leaves the patient helpless and chronically infected. We proposed that the variation of the surface antigen could be linked to the action of an integrase, similar to what exists in Borrelia, a bacteria that uses a recombination system to change its pilli’s composition, and thus avoid attack by the immune system. We have identified a tyrosine-recombinase member Pf-Int in Plasmodium falciparum, one of the causative agent of Malaria in humans (Ghorbal et al, PlosOne 2012). Through affinity chromatography of Plasmodial genome fragments bound to immobilized Pf-Int, followed by sequencing or chip hybridization, we have accumulated a small database of potential tar get sites. Simple blast searches have shown that 30 % of the sequences are from the rifin, stevor or var gene family members (encoding Rifin, Stevor and PfEMP1 proteins). These are surface glycoprotein encoding genes. We would like to identify within these A/T rich regions any common motifs that could be hidden, and resisted our attempts of sequence alignment with classical methods. This will help us design short oligonucleotides which will serve as substrate for Pf-Int, and the complex obtained used to form crystals in the process of determining the three dimensional structure by x-ray crystallography. The second step is to use the target sequences to search the genome to identify other similar sites, and therefore bring light on the physiological role of Pf-Int. Recombinases bind in a symmetric fashion to their target sites. With one dimer bound per DNA, thus one monomer per half site. Identifying the molecular details of the bound complex will help us design methods to b lock the recombination event, thus removing variation.