BACKGROUND: Investigations showed different effects of magnetic fields (MFs) on the immune system. During humoral immune responses, genes of activation-induced deaminase (AID) and B-cell lymphoma-6 (Bcl-6) are expressed and interleukin (IL)-6 and IL-21 are produced. These factors play significant roles in class switching, affinity maturation of antibodies and activations of B cells germinal centers (GCs). Therefore, this study investigated the effect of 50-Hz MFs exposure with different densities on these factors. MATERIALS AND METHODS: Eighty rats were divided into four exposures and control groups. The treatment groups were exposed to magnetic flux densities of 1, 100, 500, and 2000 μT (50 Hz, 2 h/d for 60 d). To activation of the immune system, all the animals were immunized with human serum albumin on days 31, 44, and 58 of exposure. Reverse transcription-quantitative polymerase chain reaction was used to assay the expression levels of AID and Bcl-6 genes in the spleen. The serum levels of IL-6 and IL-21 were also detected by enzyme-linked immunosorbent assay at the pre-and post-immunization phases. RESULTS: AID expression was significantly declined at 1μT magnetic flux density, while no change was observed in the expression of Bcl-6. Serum IL-6 was increased only in the 500 μT group at the post-immunization phase. CONCLUSIONS: It seems exposure to 50-Hz MFs at 1 μT density, suppresses AID and may cause a decline in class switching and affinity maturation of Abs. On the other hand, exposure to 500 μT, may activate them. These findings demonstrate the various potential effects of MFs on the humoral immune system.