Large intragenic deletions within the DMD locus account for about 60% of Duchenne and Becker muscular dystrophy patients. Two deletion hot-spots have been described in the dystrophin gene, but the mechanisms that determine chromosome breaks in these regions are unknown, and the huge dimensions of the gene have hampered the description of a consistent number of breakpoint sequences. A long-distance polymerase chain reaction strategy was used to amplify 20 deletion junctions involving the major hot-spot and to describe breakpoint position at the sequence level. These junctions were analyzed together with previously reported breakpoint locations so as to increase the sample number and possibly provide a comprehensive study. Minisatellite core sequences, chi elements, translin-binding sites, Pur elements, and matrix attachment regions were sought over the whole gene. Sequence-dependent DNA curvature and duplex stability were also calculated throughout the gene, and their cumulative frequency distribution was evaluated. No association with either sequence or structure elements involved in known illegitimate recombination mechanisms was identified. This study highlights the importance of a whole gene approach to rule out the presumptive role of specific features that, when locally analyzed, might suggest involvement in gene rearrangements.