The deletion of the long arm of chromosome 6 is the most common cytogenetic abnormality in Waldenstrom's macroglobulinemia (WM), but its prognostic significance is unclear. We investigated 77 patients with WM by interphase cytoplasmic immunoglobulin M fluorescence in situ hybridization (cIgM-FISH) and correlated the 6q status with the patients' clinical features and survival. cIg-FISH detected hemizygous 6q deletions in 32 patients (41.6%). The 6q deletions were correlated with higher C-reactive protein levels (P = .02) and CD23 expression (P = .03) but not with other clinical laboratory features of WM. There was no significant difference in time to the initial treatment between deleted and non-deleted groups (median, 5.6 months vs. 2.6 months; P = .46), or overall survivals in patients with and without del (6q) (163 months vs. not reached; P = .83). Our study confirms that the 6q deletion is a frequent event, but it does not appear to affect the clinical outcome of WM.