Subtraction hybridization was used to identify sequences of Mycobacterium bovis DNA which might be of diagnostic value. Genomic DNA from Mycobacterium avium, isolated commonly from cattle and whose tuberculin is used in the comparative intradermal tuberculin test, was subtracted from M. bovis genomic DNA. A novel sequence, of 131 bp, which appears to be Mycobacterium tuberculosis complex-specific was identified. The specificity of this sequence was stringently tested by a probe and polymerase chain reaction (PCR) assay. Nucleotide identity determination and sequence comparisons revealed that the 131-bp sequence is located directly upstream of a potential isocitrate dehydrogenase (IDH) coding gene and may be of diagnostic value, enabling differentiation of M. tuberculosis complex mycobacteria from other mycobacterial species.