Background: Side population (SP) cells are characterized by the ability to exclude Hoechst 33342 dye due to high expression of the ATP-binding cassette transporter. This ability is associated with drug-resistant characteristics of cancer stem cells. Methods: We analyzed SP cells from human B-cell non-Hodgkin’s lymphoma cell lines and primary cells derived from patients and compared them with non-SP (NSP) cells. Results: SP cells comprised a minor fraction of all cells ranging from 1.5 ± 1.8 to 8.3 ± 5.7% in cell lines and had higher ABCG2 expression than NSP cells. SP cells had better cell viability, colony-forming ability and drug resistance than NSP cells. The SP cells also showed stem cell-like characteristics, including elevated telomerase activity and higher expression of OCT4 and NANOG. A cDNA microarray demonstrated that SP cells had decreased expression of genes associated with apoptosis and cell death compared to NSP cells. Conclusions: The presence of SP cells might imply the possibility of lymphoma stem cells and be associated with a malignant potential of B-cell lymphoma.