It has been suggested that microbial agent(s) are involved in the onset of Crohn's disease. None of the candidates, however, has been unequivocally demonstrated to be a causative agent. The macroscopically earliest lesion takes place in the lymph follicle, irrespective of the initial attack or relapse in Crohn's disease. Human leucocyte antigen-DR (HLA-DR) antigens are expressed on the epithelium around the lymph follicle even in areas endoscopically uninvolved in Crohn's disease. These observations make the lymph follicle critical in the onset of Crohn's disease. The lymph follicle is a port of entry of a variety of microbial agent(s), leading to the speculation that microbial agent(s) exist in the lymph follicle. Polymerase chain reaction (PCR) using universal primers designed from conserved regions of bacterial ribosomal RNA or techniques such as representational difference analysis, may well identify microbial agent(s) in the lymph follicle that are specific to Crohn's disease. The existence of bacteria in the lymph follicle is here indicated by preliminary studies.