A research program has been undertaken to investigate the pathogenesis of M. paratuberculosis and M avium in deer and to determine those antigens that elicit specific humoral and cellular immune responses. A number of recombinent clones expressing immunogenic antigens have been isolated from a gt11 genomic library of M. paratuberculosis using sera from clinically infected or experimentally inoculated animals. The recombinent clones have been lysogenized in Escherichia coli Y1089 and the M. paratuberculosis antigens encoded by the clones have been identified using antibody eluted from fusion protein bands on Western blots. The recombinant clones contain DNA sequences coding for antigens of approximately 33 kd and 28 kd and for the 70 kd heat shock protein. In addition, a soluble protein of 30 kd has been purified from M. paratuberculosis cell lysates which elicit strong humoral and cellular immune responses in infected animals. The N-terminal amino acid sequence of this protein has been shown to share 90% homology with those of the mature 30 kd alpha-secretory antigens of M. bovis and M. kansasii and also with a 32 kd secretory antigen of M. tuberculosis.