Background: Fluorescent silica nanoparticles have been extensively utilised in a broad range of biological applications and are facilitated by their predictable, wellunderstood, flexible chemistry and apparent biocompatibility. The ability to couple various siloxane precursors with fluorescent dyes and to be subsequently incorporated into silica nanoparticles has made it possible to engineer these fluorophores-doped nanomaterials to specific optical requirements in biological experimentation. Consequently, this class of nanomaterial has been used in applications across immunodiagnostics, drug delivery and human-trial bioimaging in cancer research. Main body: This review summarises the state-of-the-art of the use of dye-doped silica nanoparticles in bioapplications and firstly accounts for the common nanoparticle synthesis methods, surface modification approaches and different bioconjugation strategies employed to generate biomolecule-coated nanoparticles. The use of dye-doped silica nanoparticles in immunoassays/biosensing, bioimaging and drug delivery is then provided and possible future directions in the field are highlighted. Other non-cancerrelated applications involving silica nanoparticles are also briefly discussed. Importantly, the impact of how the protein corona has changed our understanding of NP interactions with biological systems is described, as well as demonstrations of its capacity to be favourably manipulated. Conclusions: Dye-doped silica nanoparticles have found success in the immunodiagnostics domain and have also shown promise as bioimaging agents in human clinical trials. Their use in cancer delivery has been restricted to murine models, as has been the case for the vast majority of nanomaterials intended for cancer therapy. This is hampered by the need for more human-like disease models and the lack of standardisation towards assessing nanoparticle toxicity. However, developments in the manipulation of the protein corona have improved the understanding of fundamental bio-nano interactions, and will undoubtedly assist in the translation of silica nanoparticles for disease treatment to the clinic.