Lanthanide ions exhibit unique luminescent properties, including the ability to convert near infrared long-wavelength excitation radiation into shorter visible wavelengths through a process known as photon upconversion. In recent years lanthanide-doped upconversion nanocrystals have been developed as a new class of luminescent optical labels that have become promising alternatives to organic fluorophores and quantum dots for applications in biological assays and medical imaging. These techniques offer low autofluorescence background, large anti-Stokes shifts, sharp emission bandwidths, high resistance to photobleaching, and high penetration depth and temporal resolution. Such techniques also show potential for improving the selectivity and sensitivity of conventional methods. They also pave the way for high throughput screening and miniaturization. This tutorial review focuses on the recent development of various synthetic approaches and possibilities for chemical tuning of upconversion properties, as well as giving an overview of biological applications of these luminescent nanocrystals.