Advanced bioanalysis, including accurate quantitation, has driven the need to understand biology and medicine at the molecular level. Bioconjugated silica nanoparticles have the potential to address this emerging challenge. Particularly intriguing diagnostic and therapeutic applications in cancer and infectious disease as well as uses in gene and drug delivery, have also been found for silica nanoparticles. In this review, we describe the synthesis, bioconjugation, and applications of silica nanoparticles in different bioanalysis formats, such as selective tagging, barcoding, and separation of a wide range of biomedically important targets. Overall, we envisage that further development of these nanoparticles will provide a variety of advanced tools for molecular biology, genomics, proteomics and medicine.