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This review highlights and addresses issues related to research on the development of mesoporous silica nanomaterials (MSNs) based nanodevices for biological applications. Through the review, a variety of synthetic routes and surface functionalization is first introduced with regard to the preparation of MSNs with different chemical and physical features. Then, the effects of their various structural and compositional features on the induced biological activities are described, as recent biological applications of MSNs are summarized, typified by drug/biomolecule delivery, bioimaging, biocatalysis and biosensing. Conclusions are reached and prospects in the field are also envisioned.