Performing a genome wide scan by SNP microarray on a Jordanian consanguineous family where five brothers were diagnosed with complete globozoospermia, we show in a first study that the four out of five analysed infertile brothers carried a homozygous deletion of 200 kb on chromosome 12 encompassing only DPY19L2. The gene encodes for a transmembrane protein and is surrounded by two low copy repeats (LCRs). Very similar deletions were found in three additional unrelated patients. Later, we have pursued our patient screen by recruiting a largest cohort of patients. Out of a total of 54 patients analysed, 36 (66.7%) showed a mutation in DPY19L2. Out of 36 mutated patients, 20 are homozygous deleted, 7 heterozygous composite and 4 showed a homozygous point mutation. We characterized a total of nine breakpoints that clustered in two recombination hotspots, both containing direct repeat elements. These findings confirm that the deletion is due to a nonallelic homologous recombination (NAHR) between the two LCRs. Thus, Globozoospermia can be considered as a new genomic disorder. This study confirms that DPY19L2 is the major gene responsible for globozoospermia and enlarges the spectrum of possible mutations in the gene.