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We examined 13 cases of the primary central nervous system malignant lymphoma (PCNSML) with established histological diagnosis and valid clinical information to clarify the clinicopathologic characteristics of PCNSML. All tumors were classified according to the World Health Organization as diffuse large B-cell lymphoma (DLBCL), and four were positive for CD 10 or BCL-6. All of the tumors had a high proliferative activity containing 15.7% to 84.8% (mean = 59.8%) MIB-1 positive cells, although there was no correlation between MIB-1 staining indices and the survival period of patients. Molecular analysis using PCR demonstrated clonal rearrangement of the IgH gene in the majority of cases analyzed (9/10 = 90%). Tumor cell apoptosis was consistently demonstrated by the routinely-processed histology and the immunohistochemistry for single-stranded DNA, and apoptotic cells were engulfed by phagocytic macrophages. These findings indicate that the majority of this series of PCNSML were DLBCL with high proliferative activity and clonal B-cell process and that a subset of the cases are of putative germinal center B-cell origin. Since there was no statistical correlation between the histopathological finding and the survival rate, additional studies, including quantitative investigation for the extent of apoptotic cells, in large numbers of patients are required.