Complex chromosomal rearrangements (CCR) include diverse structural anomalies leading to complex karyotypes which are difficult to interpret. Although karyotype analysis has been able to identify a large number of these rearrangements and to distinguish de novo and familial events, it is the advent of molecular cytogenetic and sequence analysis techniques which have led to an understanding of the molecular mechanisms underlying the formation of CCR. The diversity and high level of complexity inherent to CCR raises questions about their origin, their ties to chromosome instability and their impact in pathology. Today it is possible to precisely characterize CCR and to offer carriers sophisticated diagnostic techniques, such as preimplantation diagnosis. However, the meiotic segregation of these rearrangements remains very complex.