Shrimp farming is an economic activity. Its aim is to make money. Efficient management of a shrimp production unit, therefore, requires that if antimicrobial agents are used they should be administered only when there are reasonable grounds for believing that the economic gains that may be expected, as a result of their administration, will be greater than the costs associated with that administration. The first section of this chapter addresses some of the issues that must be considered in undertaking the formal or informal cost-benefit analysis that must precede the initiation of any administration of antimicrobial agents. The second section focuses on the extent to which support laboratories can assist the health care professionals and farmers in making appropriate decisions within this cost-benefit analysis. This section provides an evaluation of the laboratory methods for measuring the antimicrobial susceptibility of bacteria associated with shrimp diseases and how the meaning of the data generated by these tests can be established. The final section addresses the science behind the arguments that have been made that the use of antimicrobial agents in aquaculture in general, and in shrimp farming in particular, has had, or could have, an adverse impact on human health or the environment. It analyses the mechanisms by which such impacts could be mediated and provides a critical evaluation of the currently available data.