We investigated chromosomal alterations using comparative genomic hybridization (CGH), and DNA ploidy patterns using laser scanning cytometry (LSC) in 8 primary central nervous system lymphomas (PCNSLs). The average number of chromosomal alterations detected by CGH was 6.9 (gain: 4.1, deletion: 2.8). Frequent alterations were gains of chromosomes 12, 18q, and X, and deletion of 6q, which were similar to those seen in non-CNS diffuse large B-cell lymphoma. DNA aneuploidy was detected by LSC in 4 of the 8 cases. The DNA aneuploid lymphomas had more chromosomal alterations than the DNA diploid ones (9.3 vs. 4.5, P <.05). The former had higher MIB-1 indices than the latter. The present investigation indicates that although most of the PCNSL are histologically uniform, they are divided cytogenetically into DNA aneuploid and diploid tumors.