Secretory IgA is the most abundantly produced Ig in different mucosal tissues, such as the gastrointestinal tract and the salivary glands. These mucosal tissues are considered to be part of the common mucosal immune system. The specificity and immunoglobulin (Ig) VH gene repertoire of the IgA producing cells of both tissues is still largely unknown. To investigate the diversity of the antibody repertoire of IgA producing cells at different mucosal effector sites, we analysed used Ig VH genes by H-CDR3 spectrotyping and VH gene sequencing of both ileum and salivary gland IgA producing cells of PVG rats. Both types of tissues showed a limited diversity for the two major VH gene families, J558 and PC7183. The salivary gland showed even less diversity than the ileum of the same rat. Cloning and sequencing of used IgA VH genes confirmed the very restricted usage of VH genes since multiple sets of clonally related sequences in both types of tissues were found. More clones were found in salivary gland than in ileum and both tissues did not have shared VDJ joining regions. IgA derived from salivary gland used germline or near germline VH genes, whereas the ileal VH genes contained more mutations. Furthermore, clonal evolution patterns from all analyzed VH gene sequences of the salivary gland IgA producing cells show mainly randomly acquired somatic mutations, in contrast to the clonal evolution patterns often observed as a consequence of affinity maturation in germinal center reactions in peripheral lymphoid organs and Peyer's patches. Our results imply that IgA producing cells in the salivary gland are neither induced at the same place nor selected in the same way as the IgA producing cells in the ileum. The function of the IgA secreted by salivary gland is very likely a first line of defense with (near) germline encoded IgA, whereas in the intestine the majority of utilized IgA VH genes show evidence of somatic hypermutation.