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Luminescence probe has been broadly used for bio-imaging applications. Among them, near-infrared (NIR) quantum dots (QDs) are more attractive due to minimal tissue absorbance and larger penetration depth. Above said reasons allowed whole animal imaging without slice scan or dissection. This review describes in vitro and in vivo imaging of NIR QDs in the regions of 650–900 nm (NIR-I) and 1000–1450 nm (NIR-II). Also, we summarize the recent progress in bio-imaging and discuss the future trends of NIR QDs including group II-VI, IV-VI, I-VI, I-III-VI, III-V, and IV semiconductors.