The emergence of the aggregation-induced emission (AIE) concept significantly changes the cognition of the scientific community toward classic photophysical phenomena. More importantly, the AIE phenomenon has brought huge opportunities for the analysis of bioactive species, the monitoring of complicated biological processes, and the elucidation of key physiological and pathological behaviors. As a class of promising luminescent materials, AIE luminogens (AIEgens) are weakly or non-emissive in the form of isolated molecular species but emit particularly strong fluorescence in the aggregated and solid states. Motivated by the prominent advantages such as high brightness, large Stokes shift, excellent photostability, and good biocompatibility, AIEgen-based bioprobes have been widely explored in the field of biomedicine. This review aims to provide a systematic summary of the developmental history and an in-depth perspective of the current landscape of AIE in the biomedical field, with an emphasis on the discussions of major working principles. The milestones of the historical development of AIE in the biomedical field are first reviewed. A total of four major research directions are then extracted, including biomacromolecule sensing (at the molecular level), in vitro cell imaging (at the cellular level), in vivo imaging (at the animal level), and cancer theranostics (at the cellular and animal levels), together with clear-cut tables showing comprehensive cases for further study. Lastly, this review is concluded by the discussions of several perspectives on future directions. It is believed that AIEgen-based bioprobes will play vital roles in the exploration of mysterious life processes by integration with various cutting-edge modalities and techniques with an ultimate goal of addressing more healthcare issues.