Semiconductor quantum dots (QDs) as newly developed fluorescence labels are of significant importance in applications of medical and biological fields. In comparison with conventional organic fluorescence labels, QDs show super properties with adjustable fluorescence, broaden excitation and narrow emission, photochemical stability, well developed surface chemistry and bioconjugation capability, which are endowing new developing opportunities in targeting, imaging, DNA and protein detection, medicine, clinic science, biochip and biosensor in life system. This paper reviews the latest breakthrough of QDs as fluorescence labels in applications of medical and biological fields on the basis of the authors’ research works on QDs biological fluorescence imaging and toxicity, and the challenge of QDs encountered in applications of in medical and biological fields is commented as well.