Near-infrared (NIR) fluorescent probes have attracted much attention, but despite the availability of various NIR fluorophores, only a few functional NIR probes, that is, probes whose absorption and/or fluorescence spectra change upon specific reaction with biomolecules, have been developed. However, functional probes operating in the NIR range that can be targeted to protons, metal ions, nitric oxide, P-galactosidase, and cellular stress markers are expected to be effective for fluorescence imaging in vivo. This Focus Review concentrates on these functional NIR probes themselves, not their applications.