It has been suggested previously that a deficiency in mucosal immunoglobulin (Ig) A production could be involved in the pathogenesis of chronic enteropathy in German shepherd dogs (GSDs). Recent research has shown that single nucleotide polymorphisms in the gene encoding Toll-like receptor (TLR)-5 are associated with an increased risk of development of chronic idiopathic enteropathy in this breed. IgA is essential for mucosal immunity and studies in mice have linked the interaction of TLR5 with its ligand flagellin to class switching of B cells into IgA-producing plasma cells. We hypothesized that dogs carrying the risk-associated (RA) genotypes for G22A and C100T genes of TLR5 would have a different number of IgA plasma cells in the duodenal and colonic mucosa compared with dogs carrying the risk-protective (RP) genotypes. Thirty-one GSDs were diagnosed with idiopathic chronic enteropathy by clinical exclusion diagnosis and histopathological confirmation. Immunohistochemistry was performed using goat anti-dog IgA primary antibody. Two sections of duodenum, and colon if available, were examined from each animal. Twelve images were captured from each section and IgA-positive cells were counted and expressed per 10,000 μm2. TLR5 genotypes for the G22A and C100T genes were determined by polymerase chain reaction on blood samples. Numbers of IgA-positive cells in the duodenum and colon were slightly higher than those published previously for GSDs with or without chronic enteropathy (mean in the crypt area of the duodenum 52.6 ± 16.2; mean in the tip of the duodenal villus 51.12 ± 3.83; mean in the base of the duodenal villus 55.02 ± 3.3; mean in the crypt area of the colon 67.4 ± 4.3). There was no correlation between numbers of IgA-positive cells in duodenum or colon between dogs carrying the RA versus the RP alleles of TLR genes. Further studies are needed to assess the production of secretory IgA and its relationship to TLR5 genotypes.