BACKGROUND It is a well-established fact that cigarette smoking causes degenerative, inflammatory, and respiratory diseases in humans. Because many factors such as air pollution and harsh working conditions can easily be eliminated in animal studies, we conducted this study to identify the effect of tobacco on rat trachea. METHODS 24 male Wistar rats were divided randomly into an experimental and a control group. The experimental group of rats was exposed to cigarette smoke for 2 h each day over a duration of 60 consecutive days and the control group was treated in an identical fashion yet exposed only to room air. A morphometric study was performed on tracheal specimens taken from 22 rats (10 smoke-exposed rats and 12 control rats). RESULTS Our results show that many of the morphological changes of the tracheal epithelium were found in the experimental group and significant quantitative differences were observed between the two groups. Loss of cilia, basal cell hyperplasia, goblet cell hyperplasia and an increased number of subepithelial inflammatory cells were observed by light microscopic examination of the trachea of experimental rats. We found very high levels of plasma thiocyanate after exposure to smoke in the experimental group, but no increase in the control group. CONCLUSIONS The oxidants contained tobacco which could play an important role in the development of these structural and functional abnormalities in the trachea after smoke exposure. In addition, smoking can recruit inflammatory cells to the trachea.