Bacterial DNA motifs (such as CpG-oligodeoxynucleotides: CpG-ODN) induce innate immune responses via binding to Toll-like-receptor-9 (TLR-9). In murine intestinal mucosa treatment with CpG-ODN worsens chronic intestinal inflammation, whereas it prevents or ameliorates colitis when given in a prophylactic setting. In tonsils B cells have been reported to express TLR-9, especially after activation. Whether B cells in the human intestinal mucosa also express TLR-9 and whether their function can be influenced by CpG-ODN is, so far, unknown. Mucosal B cells were isolated according to a new protocol from surgical specimens of patients with inflammatory bowel disease and from controls by collagenase digestion followed by magnetic cell sorting using anti-CD19 antibody armed magnetic beads. TLR-9 mRNA and protein expression were quantified by real-time polymerase chain reaction (PCR) and Western blot, respectively. Immunoglobulin A (IgA) secretion was measured by enzyme-linked immunosorbent assay after stimulation of isolated B cells with CpG-ODN, control GpC-ODN or lipopolysaccharide (LPS). Flow cytometric analysis of the isolated lamina propria mononuclear cells showed a purification of 73% (+/-22%) CD19(+) cells. By quantitative reverse transcription-PCR and by Western blot TLR-9 expression in this cell population was evident. IgA secretion was increased significantly by CpG-ODN incubation compared with GpC-ODN and LPS. Compared with unstimulated controls, CpG-ODN up-regulated IgA secretion to 139% (+/-21%). These data demonstrate that CD19(+) mucosal B cells express TLR-9 and secrete increased levels of IgA upon stimulation with CpG-ODN, indicating an additional link between adaptive and innate intestinal immune responses.