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Paratuberculosis disease occurs with high frequency in many places of the world and it is a chronic infection of ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to investigate the association between MAP-resistant or MAP-susceptible goats and short tandem repeats (STR) markers. Blood samples were collected from 48 adult goats (27 positive and 21 negative) of the Italian native Garfagnina goat breed from a single flock that had experienced annual mortalities due to MAP infection. Diagnosis was achieved by serological tests and by post-mortem examination of affected animals. To investigate possible genetic influences on susceptibility or resistance of goats to MAP disease, 12 STR markers were used. For each marker, allele and genotypes frequencies between MAP-positive and MAP-negative groups of animals were compared using the chi-square test and Fisher’s exact tests. In this study, two microsatellite loci SRCRSP05 and ETH10 were associated with the disease playing an interesting role in the susceptibility or resistance to the disease. Although the present study should be considered preliminary, our results reveal for the first time that two microsatellite loci were associated with the development of lesions due to  MAP in the Garfagnina goat breed.