Quantum dots (QDs) are a special type of engineered nanomaterials with outstanding optoelectronic properties that make them as a very promising alternative to conventional luminescent dyes in biomedical applications, including biomolecule (BM) targeting, luminescence imaging and drug delivery. A key parameter to ensure successful biomedical applications of QDs is the appropriate surface modification, i.e. the surface of the nanomaterials should be modified with the appropriate functional groups to ensure stability in aqueous solutions and it should be conjugated with recognition elements capable of ensuring an efficient tagging of the BMs of interest. In this review we summarize the most relevant strategies used for surface modification of QDs and for their conjugation to BMs in preparation of their application in nanoplatforms for luminescent BM sensing and imaging-guided targeting. The applications of conjugations of photoluminescent QDs with different BMs in both in vitro and in vivo chemical sensing, immunoassays or luminescence imaging are reviewed. Recent progress in the application of functionalized QDs in ultrasensitive detection in bioanalysis, diagnostics and imaging strategies are reported. Finally, some key future research goals in the progress of bioconjugation of QDs for diagnosis are identified, including novel synthetic approaches, the need for exhaustive characterization of bioconjugates and the design of signal amplification schemes.