An accurate, rapid and cost-effective diagnosis is the cornerstone of efficient clinical and epidemiological management of infections. Here we discuss the relevance of an emerging technology, multiplexed immunoassays read by flow cytometry, for the diagnosis of infectious diseases. In these assays, multiple fluorescent microspheres, conjugated to different antigens or antibodies, constitute the solid phase for detecting antibodies or antigens in biological samples. These assays seem to be more sensitive than traditional immunoassays, have a high throughput capacity, and provide a wide analytical dynamic range. Additionally, they have multiplexing ability-ie, they are capable of measuring multiple antibodies or antigens simultaneously. We discuss four different areas where this technology could make an impact in resource-poor settings: (i) infections causing rash and fever in children; (ii) seroepidemiological studies on vaccine-preventable diseases; (iii) management of genital ulcers and vaginal discharge; and (iv) screening of infections in blood banking. We predict a widespread use for a new breed of small, affordable, practical flow cytometers as field instruments for replacing ELISA and RIA tests, which will also be capable of doing cellular immunological tests such as CD4+ T-cell enumeration and Plasmodium falciparum detection in whole blood.