The imaging techniques of the cornea and anterior segment such as corneal topography, optical coherence tomography (OCT) and ultrasound biomicroscopy (UBM) provides a detailed information on corneal curvature and a cross section of macroscopic anatomy. The confocal microscopy has advanced to allow analysis of microscopic morphology of the cornea in vivo. The noninvasive nature of in vivo confocal microscopy (IVCM) allows for a rapid examination of a patient’s cornea in its physiologic state and allows for repeat examinations of the same tissue over time, while avoiding artifacts associated with ex vivo study. The chapter here discusses in detail about the principles of confocal microscopy, its clinical use and applications, research applications, and limitations.