Human antigen presenting cells commonly express CD4 but the significance of this phenomenon has not been clarified. We analyzed a panel of Epstein-Barr virus-immortalized B cells (so called lymphoblastoid cell lines, LCL) by using flow cytometry, DNA-microarray analysis, and reverse transcriptase-polymerase chain reaction (RT-PCR). The number of CD4(+) cells varied from cell line to cell line but expression of CD4 was detected by flow cytometry and RT-PCR in all investigated cell lines. To characterize CD4 expressing LCL in more detail, we separated CD4(+) and CD4(-) cells from single cell lines by using immunomagnetic beads. When we cultured sorted CD4(+) and CD4(-) cells, we observed that CD4 expression was stable for several passages. However, the number of CD4(+) cells decreased with time in culture. We never observed that CD4(-) cell lines returned back to a CD4(+) phenotype. DNA-microarray analysis of isolated CD4(+) and CD4(-) cells indicated that the overall gene expression profile of both cell populations was highly similar. In addition, CD4(+) and CD4(-) cells showed the same allostimulatory capacity. CD4(+) LCL showed a slightly increased interleukin-16 induced chemotaxis. Differences in the gene expression profile of CD4(+) and CD4(-) cell lines suggested that loss of CD4 expression occurred during a differentiation step involving achaete-scute complex homolog-like 1.