Intracellular diseases are difficult to treat and constitute a major problem for modern medicine. In this type of diseases, a TH-1 immune response favors protection, while a TH-2 response is detrimental to the host. Current vaccines are using antigens to initiate an immune response regardless of its nature and its mechanism. New vaccines are designed to combine selected antigens with potent adjuvants to stimulate the appropriate pathway of the immune system and deliver a lasting protective immunity. The Mycobacterium recombinant vaccine system for treatment of intracellular diseases utilizes antigen delivery systems in the form of non pathogenic Mycobacterium strains, genetic transfer systems in the form of cloning and expression vectors, and related technologies to provide products containing non toxic immuno-regulating Mycobacterium adjuvants, non toxic immuno-stimulating exogenous antigens specific for a variety of diseases, and non toxic amounts of cytokines that boost the TH-1 pathway. The cloning and expression Mycobacterium vectors include both pAL5000-based extra-chromosomal and D29-based integrative vectors.