Peptides, proteins, and nucleotides or DNA fragments are the new generation of drugs. They are becoming attractive owing to the fast development of biotechnology. The admnistration of such molecules, however, may be a problem as sensitivity to temperature, instability at some physiological pH values, short plasma half-life, and high molecular dimension, which hinders the diffusive transport, make, at the moment, parenteral route the only possible way of administration of such molecules. Controlled drug delivery that comprises the development of new administration routes could be the answer to the problems for administration of biotechnological molecules. The rational of drug delivery is to change the pharmacokinetic and pharmacodynamic of drugs by controlling their absorption and distribution. Rate and time of drug release at absorption site could be programmed using a so called delivery system. Different technologies, such as chemical (pro-drugs), biological, polymers, lipids (liposomes, LDL), have been proposed to obtain controlled drug release. Also the use of new administration routes is part of controlled drug delivery. In fact, it could increase the drug absorption and reduce the effects of the active ingredient in those districts not interested in the therapy. Drug delivery systems allowing for an effective release in vivo of new biotechnological molecules, such as recombinant antiidiotypic antibodies with antibiotic activity, devoted to the treatment of pulmonary (tuberculosis and pneumocystosis) and mucosal (candidiasis) diseases are discussed under that perspective.