Fluorescence optical imaging is a highly sensitive and powerful tool with diverse in vitro and in vivo applications for preclinical and clinical studies. This review is focused on the optical imaging in the near-infrared (NIR) region since improved signal-to-noise ratio and deeper penetration of light through tissues could be achieved due to the minimal autofluorescence and reduced light scattering at these wavelengths. In particular, imaging agents absorbing and emitting in the biological diagnostic window (650–1450 nm) are discussed. The photophysical properties and particularities of chemical structures or compositions of four different families of probes : (i) organic fluorophores, (ii) fluorescent proteins (FPs), (iii) semi-conductor nanocrystals (quantum dots) and (iv) lanthanide(III)-based complexes and nanomaterials are presented. Advantages and drawbacks, commercial availability and toxicity as well as selected applications of these probes are discussed. A specific attention is given to lanthanide(III)-based compounds due to their unique optical properties, e.g. sharp emission bands with minimal sensitivity to the microenvironment, large differences between excitation and emission wavelengths and strong resistance toward photobleaching. The use of such probes brings additional perspectives and facilitates developments of novel strategies in optical imaging including real-time experiments and new approaches for diagnostic.