Microorganisms, including bacteria, viruses and fungi, are ubiquitous in nature. Some are extremely beneficial to life on Earth, whereas some cause diseases and disrupt normal human physiology. Pathogenic microorganisms can also undergo mutations and develop resistance to antimicrobial agents, which complicates diagnostic and therapeutic regimens. This calls for continuing efforts to develop new strategies and tools that can provide fast, sensitive and accurate diagnosis, as well as effective treatment of ever-evolving infectious diseases. Aggregation-induced emission luminogens (AIEgens) have shown promise in imaging, identification and inhibition of various microbial species. Compared to conventional organic fluorophores, AIEgens can offer improved photostability, and have found utilities in imaging microorganisms. AIEgens have been shown to detect microbial viability and differentiate among different microbial strains. Theranostic AIEgens that integrate imaging and killing of microbes have also been developed. This review highlights examples in the literature where AIEgens have been employed as molecular probes in the imaging, discrimination and killing of bacteria, viruses and fungi.