We assessed the prognostic impact of occult bone marrow involvement, determined by flow cytometry and/or polymerase chain reaction, in a population of 117 consecutive patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL) treated with rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP). Twenty-four (20.5%) had morphologically diagnosed and 16 (13.7%) had occult marrow involvement, and 77 (65.8%) had no marrow involvement. Although the pretreatment characteristics of the negative or occult marrow involvement group were similar, severe hematological toxicity after R-CHOP was more frequent in the occult marrow involvement group. Progression-free survival (PFS; p = 0.015) and overall survival (OS; p = 0.035) for the occult marrow involvement group were significantly shorter than those for the negative group, and were comparable to those of the morphologic marrow involvement group, independent of the International Prognostic Index score for PFS. Occult bone marrow involvement predicts severe hematological toxicity and negatively impacts on the PFS and OS of R-CHOP therapy.