The formation of small supernumerary marker chromosomes (sSMC) became much clearer during recent years. Nowadays, it is suggested that majority of all kinds of de novo sSMC (inverted duplication-, ring-, and centric-minute-shaped-ones) are products of incomplete trisomic rescue during early embryogenesis. Recent work, based on molecular cytogenetics, suggests that these trisomic rescue events are going together with chromothripsis, directed against the supernumerary chromosome to be degraded. Here, we present a protocol on how to characterize the so-called discontinuous sSMC by means of fluorescence in situ hybridization.