Purpose Balanced chromosomal translocations are found in one out of 500 subjects in the general population. They usually do not carry any phenotypic consequences, except for possible infertility and for the production of unbalanced gametes leading to spontaneous abortions or chromosomal syndromes in the offspring. An association between chromosomal rearrangements and increased apoptosis markers has been demonstrated on a global scale in sperm samples of translocation and inversion carriers. In order to specify which kind of sperm cells is subject to an increased apoptosis process, this present study was aimed to analyse both chromosomal segregation and DNA fragmentation, sperm cell by sperm cell. Methods Six patients carrying a chromosomal rearrangement (three reciprocal translocations, two Robertsonian translocations, and one chromosomal pericentric inversion) were included in a retrospective manner. Both DNA fragmentation and chromosomal segregation in spermatozoa were evaluated simultaneously using a modified TUNEL assay associated with FISH. Two thousand spermatozoa were analysed for each patient. ResultsWe showed a higher proportion of spermatozoa with fragmented DNA among the unbalanced sperm cells, compared to the balanced ones, in all six patients. Conclusions These results suggest an increased fragility of unbalanced spermatozoa to exogenous fragmentation factors. The exact mechanisms of those processes remain to be elucidated.