To compare the molecular cytogenetic characteristics between Waldenström macroglobulinemia (WM) and multiple myeloma (MM), we performed interphase fluorescent in situ hybridization (FISH) in Korean patients with WM and MM. Forty patients with WM and 132 patients with MM were enrolled onto the study. FISH was performed with seven different probes: 6q21, 6q23, CEP4, CEP9, immunoglobulin (IgH) breakapart, RB1 gene, and 1q25. Out of 22 WM patients, 4 (18%) had abnormal karyotypes, mainly structural changes on conventional karyotyping. After performing FISH for the available 29 cases, deletions of 6q23 and 6q21 were newly detected in 3 cases (10%). There was no other anomaly, including trisomy 4 in WM. No 6q deletion was observed in MM patients, but RB1 deletion was the most common change (45%), followed by IgH translocation (42%) and gain of 1q (38%). In conclusion, Korean WM patients had a low rate of 6q deletion (10%) and no trisomy 4.