Modern molecular medicine encompasses the utilization of many molecular biological techniques in the analysis of disease, disease genes and disease gene function. The study of disease genes and their function in an unaffected individual has been possible by the development of recombinant DNA and cloning techniques. The term gene cloning covers a range of techniques that makes it possible to manipulate DNA in a test tube and also to return it to living organism where it function normally. The tools of gene cloning includes vectors, genes and the enzymes. Overcoming the biological and methodological obstacles posed by cell factories to the production or rDNA pharmaceuticals is a main challenge in the further development of protein-based molecular medicine. Recombinant DNA technologies might have exhausted conventional cell factories and new production systems need to be deeply explored and incorporated into the production pipeline. On the other hand, a more profound comprehension of host cell physiology and stress responses to protein production would necessary offer improved tools (either at genetic, metabolic or system levels) to favour high yield and high quality protein production. Apart from the expected incorporation of unusual mammalian hosts such as transgenic animals or plants, microbial cells appear as extremely robust and convenient hosts, and gaining knowledge about the biological aspects of protein production would hopefully enhance the performance of such hosts beyond the current apparent limitations. In this regard, not only commonly used bacteria and yeasts but unconventional strains or species are observed as promising cell factories for forthcoming recombinant drugs. Their incorporation into productive processes for human pharmaceuticals would hopefully push the trend of marketed products and fulfil the increasing demands of the pharmacological industry.