Persistent bacterial infections are causally linked to gastrointestinal cancer in people, and the concept that mucosa-associated bacteria can promote carcinogenesis is well established. Perturbation of the intestinal microbiome has been documented in cats with IBD and it seems plausible it could serve as a trigger for intestinal lymphomagenesis. It is against this background that we sought to assess the presence and localization of mucosal bacteria in biopsies from cats with histologically minimally changed small intestine (MC), lympho-plasmacytic enteritis (LPE), small (SCL), and large cell (LCL) alimentary lymphoma. Cases were identified in the histopathology database at Cornell. The spatial distribution (luminal debris, mucus, adherent to epithelium and serosa, invasion, intravascular presence) and numbers of bacteria were determined by fluorescence in situ hybridization (FISH) with the eubacterial probe EUB-338. Invasive bacteria were most frequently associated with LCL (82%). Invasion was not restricted to superficial areas of eroded or ulcerated mucosa, with translocated bacteria visualized in vessels and/or the serosa of 30% LCL. These results reveal that alimentary lymphoma is associated with alterations in the number and spatial distribution of mucosa-associated bacteria. They support the need for further study to speciate lymphoma associated bacteria, and careful evaluation of cats with alimentary lymphoma for evidence of septicemia.