Nowadays luminescent semiconductor quantum dots (QDs) are widely applied in different areas due to their unique optical properties. QDs can be used as photoluminescent labels with excellent possibilities for high-throughput detection and diagnostics. For most of such applications QDs must be coupled to biomolecules, which often represents a fundamental challenge. Although QDs have a lot of advantages over organic dyes, most of the techniques that have been developed for QD functionalization and bioconjugation, are more complicated than the corresponding techniques for organic fluorescent dyes. Here, the importance of choosing a suitable bioconjugation strategy in different applications, such as imaging and assays is described. The main goal of this review is to give a structured and detailed overview and comparison of the most widely used conjugation strategies in function of the active groups (carboxyl, amine, thiol, epoxy, hydroxyl and aldehyde groups) present on QD surface.