To study the cellular morphological characteristics and changes of corneal endotheliitis by corneal microstructure in vivo.Forty-eight clinical diagnosed patients of corneal endotheliitis were examined by in vivo confocal microscopy. Confocal images of different layers were collected and observed. Of all the patients, 39 were disciform and 9 were diffuse. The history of the 48 patients was from 7 days to 23 years and the duration was from 4 to 180 days.Epithelium revealed cellular edema, enlarged intercellular gaps, and bubble between the cells. The density of sub-basal nerve plexus was significantly lower than that of normal, even disappeared in 24 patients. A numerous dendritic cells (Langerhans cells, LCs) presented in the basal epithelium layer and gradually abated with disease regression, but the density of LCs was significantly higher than that of the contralateral eye. The keratocyte revealed edema and to be activated. Inflammatory cell was found in stroma of the patients with long history and duration disease. Endothelium cells were observed edema, with enlarged intercellular gaps. Inflammatory cells was found to infiltrate into the endothelial layer, most them gathered to be keratic precipitates (KP), which were rounded or elliptic and inserted between the endothelium by pushing the endothelium away, and induced decayed area between the endothelium.Corneal endotheliitis was not only the inflammation of endothelium, but also varied pathological changes of all layer of the cornea. Corneal endotheliitis patients with long history and duration presented the mixed type with stromal keratitis. The lower density of sub-basal nerve plexus and the higher density of dendritic LCs were the characteristics of endotheliitis. Impairment of intercellular junction by KP might be another important role of cornea edema. Sufficient and accurate treatment of endotheliitis was important.