Nanofluidic system can be used as powerful tool for detecting single molecules through fluorescence correlation spectroscopy (FCS). Several types of nanofluidic channels, such as hollow nanofibres or nanotrenches, can be constructed on quartz wafers, though electrospinning and nanolithography, respectively. The advantages of nanofluidic channels in molecule detection are not only in reducing the amount of volume of analyte, but also for improving electrokinetic molecule transport. Therefore, small molecules, like proteins or DNA, can be detected in nanochannels. Furthermore, nanofluidic channels can be used to monitor protein–protein, post translational modification, protein–DNA, and protein–RNA interactions, which rely on labelling proteins of interest within fluorescent molecules, in tissue samples directly. Based on these results, nanofluidic channels can be used in diagnostic application for early diagnosis of cancers and drug screenings.