Amplification of a specific, 500-bp fragment from Mycobacterium bovis isolates and use of the fragment to differentiate between Mycobacterium tuberculosis and M. bovis was previously reported (J. G. Rodriguez, G. A. Meja, P. Del Portillo, M. E. Patarroyo, and L. A. Murillo, Microbiology 141:2131-2138, 1995). In the present study, 30 M. bovis isolates from Sardinian cattle were examined for the presence of this 500-bp fragment; 4 of the 30 isolates lacked the fragment. This result indicates that identification of M. bovis strains by amplification of the 500-bp sequence may lead to false-negative results.