Fluorescent materials have recently received great attention in biomedical research because of their good optical properties, species diversity and high sensitivity. However, most of the traditional fluorophores suffer from the aggregation-caused quenching (ACQ) effect at high concentration or in the aggregated state, which has greatly limited their biomedical applications. Fluorescent materials with the AIE effect show exactly the opposite effect to the ACQ effect, and have exhibited significant advantages in terms of tunable emission, excellent photostability and biocompatibility. In this review, we summarize current advances of AIE-based materials for biomedical applications. In particular, AIE-active biosensors for detecting biomolecules, such as hydrogen peroxide, hydrogen sulfide, biothiols and enzymes, have been summarized. Moreover, AIE-based materials applied for bioimaging, drug delivery and cancer theranostics have also been described in detail. In the last section, the future prospects and possible challenges in the development of AIE-based materials are discussed briefly.