Due to exceptional photo-physical properties, up-converting nanoparticles (UCNPs) are promising and advantageous alternative to conventional fluorescent labels used in many bio-medical applications. The first part of this review aims at presenting these properties as well as the current state-of-the-art in the up-conversion enhancement, NPs surface functionalization and bioconjugation. In the second part of the paper, the applications of UCNPs and currently available detection instrumentation are discussed in the view of the distinctive properties of these markers. Because the growing widespread use of the biofunctionalized NPs, scarce instrumentation for up-conversion detection is reviewed. Finally, the challenges and future perspectives of the UCNPs are discussed. (C) 2012 Elsevier Ltd. All rights reserved.