Proteome profiling was performed to investigate changes at a molecular level in the mouse corneal endothelium (CE) along with the basement membrane exposed to cigarette smoke (CS). Pregnant mice (gestation days 18-20) were placed in a whole-body exposure smoking chamber and a few days later pups were born. After 3½ months of CS exposure, the Confoscan4 scanning microscope was used to examine the CE of CS-exposed and control (Ct) mice. The CE was peeled under a microscope and maintained as four biological replicates (two male and two female) for CS-exposed and Ct mice; each replicate consisted of 16 CE. The proteome of the CE was investigated through mass-spectrometry using 8-plex isobaric tandem mass tags (TMT). The CE images of CS-exposed and Ct mice revealed a difference in the shape of corneal endothelial cells (CECs) accompanied by a nearly 10% decrease in CEC density (p = 3.0e-0.5) resulting from exposure to CS. The proteome profiling identified a total of 524 proteins exhibiting statistically significant changes in CE from CS-exposed and Ct mice. Importantly, proteins known to be an integral part of the basement membrane including COL4α1, COL4α2, COL4α3, COL4α4, COL4α5, and COL4α6, Col8α1, Col8α2, FN1, etc. exhibited diminished protein levels in the CE of CS-exposed mice. Here, we report the effects of CS on the CE, and our data strongly suggest that CS exposure results in reduced CEC density and diminished concentration of proteins known to be an integral part of the basement membrane.