Display omitted Near-infrared probes including dyes, nanoparticles and proteins have been particularly useful for in vivo imaging because of their ability to penetrate tissue deeper with minimal scattering and autofluorescence, opening the door to study cell biology in physiological conditions. Display omitted Taking the advantage of reduced scattering and low autofluorescence background, the NIR fluorescence probes, such as fluorescence proteins, organic molecules and nanoparticles, not only hold the promise of in vivo imaging of biological processes in physiology and pathology with high signal-to-noise ratio, but also for clinical diagnosis. In this review, we provide an overview of the recent progress on NIR probes, focusing on fundamental mechanisms of NIR dyes and nanoparticles, and protein engineering strategies for NIR proteins.