Transfusion microbiology must minimize the risks of transfusion transmitted infection (TTI) in a cost-effective and efficient manner. The wide range of transmissible microbial agents exhibits different relative risks in different circumstances; therefore, the same safety rules are not always applicable. TTIs can also exist as asymptomatic diseases in their hosts, so donors must be screened for high-risk behavior. Then blood must be screened by detecting antibodies to infectious agents. Since antibody reactivity is difficult to confirm, and cross-reactive or nonspecific effects are possible, a reactive sample can be tested by a range of assays, each based on a different immunoassay principle, or by a supplementary assay. Despite the advanced nature of these tests, problems of indeterminate donors remain, and a compromise must be made between the sensitivity and specificity of screening assays; maximum sensitivity protects transfusion recipients, but specificity prevents wasting blood or making false reports about donor health. An ideal screening assay would have maximum sensitivity, optimal specificity, simplicity, objectivity, standard format, rapid processing time, safety of reagents, and economy. Assay users must chose the best combination of available characteristics for their particular situation. For example, a French study found that 30% of seronegative, but HIV-infectious, donors are anti-HBc positive; this test would be too specific, however, in a country where hepatitis B is common. Combined assays are being used to screen for anti-HIV-1 and -2 and anti-human T-cell lymphotropic virus-I and -II; this should save time and money. Screening donors selectively (for example, Latin American migrants to North America for Trypanosoma cruzi) may protect previously unexposed populations. In some countries, transmission of HIV via seronegative blood is a problem, and HIV antigen screening and confirmation of reactivity by neutralization should occur as soon as reagents become less expensive. As test methodology continues to move through rapid developmental "generations," the development of sensitive techniques to detect nucleic acids holds promise. Several problems will remain to be solved including cost cross-contamination and carry-over in automated sampling systems, and operational and clerical errors. While there are methods to inactivate viruses in plasma pools, inactivation must incur a minimal loss of biological activity. All of these challenges are exacerbated in developing countries by a lack of resources. As physicians become knowledgeable about when to use transfusion and when to use an alternative method, such as blood salvage, refusing transfusion will be more risky than contracting a TTI.