The frequency and prognostic significance of chromosome 6q deletion were investigated in a cohort of patients with Waldenstrom macroglobulinemia (WM). By interphase cytoplasmic fluorescence in situ hybridization with probes for 6q21 and 6q25, we detected hemizygous 6q deletions in the clonal lymphoplasmacytic cells in 13 (38%) out of 34 patients. Patients with 6q deletions had a lower IgM paraprotein levels than non-deleted patients (P = 0.04). There was no correlation between 6q deletion and other clinical features of WM. There was no significant difference in overall survival between 6q deleted and non-6q deleted groups (P = 0.92). Our study confirms that 6q deletion is a frequent event, but it does not appear to be a prognostic marker for patients with WM.