The identification of marker chromosomes is important for genetic counseling. However, the origin or composition can rarely be defined with conventional cytogenetic technique alone. In this study, we investigated the incidences and types of marker chromosomes in Korean patients and attempted to establish a cost-effective diagnostic approach for marker chromosomes. We reviewed the karyotypes of 2,984 patients that were requested for the cytogenetic analysis between 1997 and 2003 at the Samsung Medical Center. Ten marker chromosomes were found and identified using fluorescent in situ hybridization (FISH). Among the ten marker chromosomes, six were supernumerary marker chromosomes (SMCs) and the rest were marker chromosomes in Turner syndrome (TS). The incidence of SMCs was 2.01/1,000, slightly higher than that previously reported. Five of six SMCs were satellited marker chromosomes. Three bisatellited marker chromosomes originated from chromosome 15 and two from chromosome 22. The origin of one SMC could not be identified. All marker chromosomes in TS originated from X- or Y chromosome. The application of FISH is indispensable to identify marker chromosomes, and the appropriate selection of probes is necessary for cost-effective analysis. For analyzing satellited marker chromosomes, application of probes for chromosome 15 followed by those for chromosome 22 is recommended and in cases of TS, probes for sex chromosomes should take precedence.