This chapter provides an overview of confocal microscopy which plays an important role in the diagnosis, prognostication, as well as evaluation of response to treatment in patients with uveitis. The confocal microscope is capable of achieving improved axial as well as lateral resolution compared to other ophthalmic devices including the slit lamp biomicroscope. The principle of the confocal microscope is based on images captured through specular reflection of light, which, in case of the cornea, accounts for less than 1% of the total light falling on the cornea. The confocal microscope has a focal lens which moves in an anteroposterior direction, shifting focus to various corneal layers and capturing images thus obtained from each plane. A small amount of light is projected on to the cornea through the condensing lens and the reflected light is captured by another lens (objective lens) that is at the same focal length as the condensing lens. A drop of a coupling medium (usually polyacrylic gel) is placed on the lens apparatus. This avoids a direct contact between the lens and the cornea, thus making it a safe procedure. The confocal microscope gives meridional sections of the living cornea. Superficial epithelial cells typically have light cell boundaries with hyper-reflective visible nuclei. A number of numerical values can be obtained using computerized analysis of the images. Although this software can be used for epithelial basal cell analysis as well, it is most appropriately used for endothelial morphological parameters. The analysis may be a fixed frame analysis or a variable frame analysis of cell size depending on the software available on the confocal microscope. Confocal microscopy enables us to visualise the severity and volume of keratic precipitates using depth values in linear scans. Endothelial ‘stress’ may occur in eyes with intraocular inflammation with resulting pathological changes which are reflected as endothelial blebs on confocal microscopy.