The objectives of this study were to estimate the presence and the dynamics of infection by Mycobacterium avium subsp. paratuberculosis in two distinct areas of Trentino both characterized by a high density of red deer and by a great number of domestic livestock (cattle and small ruminants) that share the pasture. During the five-year period 1998-2002 in the western sector of the province, the intestines of 242 red deer killed or found dead were examined. The study was extended to the eastern part of the province, in 1999, where, up to 2002, the viscera of 157 red deer were collected. M. avium subsp. paratuberculosis (MAP) was isolated in 201 of the 399 deer examined by bacterial culture (HEYM). The results obtained show a significant diffusion of MAP in the deer populations examined, with average infection prevalence of 66% and 18% in the two sectors of Trentino respectively. The typing, carried out by means of PCR-REA on the IS1311 sequence, of the identified strains as MAP by using IS900-based PCR techniques, confirmed the cattle origin of the strains isolated in the deer, suggesting a risk of transmission of the infection between domestic and wild animals due to pasture contamination. Nevertheless the disease concerns other sympatric species of wild ungulates coming from both areas under study such as roe deer, chamois and ibex, as well as non-ruminant species such as fox and hare. In order to verify if a species-specific cycle of MAP exists, phylogenetic analysis by AFLP was carried out to understand the possible role of each wild species in the epidemiology of paratuberculosis in the area.