Banana streak virus (BSV) sequences are integrated in the nuclear genome of Musa species. There is strong experimental evidence that some of these BSV integrated sequences, preferentially restricted to Musa balbisiana chromosome (noted B) and called BSV endogenous pararetrovirus (BSV EPRVs), can give rise to infectious episomal BSV particles upon stress conditions such as either inter-specific genetic crosses or in vitro micro propagation. As part of an international effort within the Musa Genomics Consortium aimed at defining the integration patterns of BSV EPRVs into Musa nuclear genome and the mechanisms leading to their activation, three BAC libraries were constructed and characterized from M. acuminata Cavendish (AAA), M. acuminata Calcutta 4 (AA) and M. balbisiana PKW (BB) nuclear genomes, respectively. Complete genomes of four BSV strains (BSV-Ol "Obino L'Ewai", BSV-Gf "Gold Finger", BSV-lm "Imove", BSV-Mys "Mysore") were used as probes to screen the BAC libraries. Upon screening of the M. balbisiana PKW BAC library, 10 BAC clones positive for BSV-OI, 9 for BSV-Gf, 26 for BSV-Mys and 24 for BSV-lm were identified. All positive BAC clones were distinct from each other. On the other hand, screening of either M. acuminata Calcutta 4 or M. acuminata Cavendish BAC libraries with the four complete viral sequences revealed that no BSV EPRVs related to the four analyzed strains were present in any of the two Musa A genomes analyzed. BAC clones found positive upon screening were further characterized by BAC-end sequencing and RFLP-fingerprinting approaches, and 6 selected BACs containing BSV-Ol or BSV-Gf EPRV sequences were completely sequenced. Detailed analysis of the nucleotide sequences and chromosomal organization of BSV-OI and BSV-Gf EPRV sequences within these BAC clones will be presented and discussed. This study represents one of the first steps towards the characterization of the mechanisms leading to the activation of BSV EPRV sequences in Musa and the impl