We report for the first time the characterization of disease-causing exonic rearrangements in the large-sized gene encoding dysferlin. A newly developed kit for multiplex ligation-dependent probe amplification analysis of the dysferlin gene was used for a total of 12 samples from patients with suspected diagnosis of primary dysferlinopathy. This analysis and subsequent genomic quantitative real-time PCR evidenced exonic rearrangements in five patients, including four different exonic deletions and one duplication. Altogether, our findings confirm the existence of exonic rearrangements as disease-causing mutations in primary dysferlinopathies.