The aims of this study are to establish a small animal model for the study of Mycobacterium avium subsp. paratuberculosis (MAP) infection, and to elucidate the mechanism of infection and fecal shedding of MAP, instead of a time consuming bovine experimental model. Guinea pigs were inoculated intraperitoneally with different species or subspecies of mycobacterium in order to characterize MAP infection. We have found that the inoculated organisms aggregate in the duodenum, and are excreted into feces within 24 hours after inoculation. Because it has been reported that the aggregation of macrophages in the tip of intestinal villi of guinea pigs, the macrophages ingested organisms seems to be involved in this in vivo dynamics of inoculated mycobacterium. Furthermore, thickening of the duodenum caused by infiltration with marked inflammatory cells and granulomas in the lamina propria mucosa have been observed after two months in guinea pig infected with MAP. Besides, exhaustive analysis of differentially expressed genes in the duodenum from infected and non-infected guinea pigs was performed by DNA microarray, and found Regenerating islet-derived 3 gamma which is one of the unique host gene expression characteristic for MAP infection. These histpathological, bacteriological and molecular biological results may be useful for understanding mycobacterium infections including MAP.