We aimed to determine the effects of water-pipe smoking on lung mucociliary clearance system using radioaerosol ventilation scintigraphy and compare with cigarette and passive smoking and determine the level of exposure to tobacco smoke by measuring urinary cotinine in each group. Volunteer water-pipe only and cigarette only smokers from various cafés in Izmir city and passive smokers as control group were included in the study after exclusion and inclusion criteria. The ages, type of smoking, duration and daily amount of tobacco smoked and the medical histories of the volunteers were noted down. The pulmonary function tests (PFT), technetium-99m inhalation scintigraphy and urinary cotinine measurement with enzyme immunoassay (EIA) and were performed for each participant. Twenty water-pipe smokers, 23 cigarette smokers and 15 passive smokers were included into the study. There were no statistically significant differences among the mean ages, BMI and PFT parameters of all participants in study and control groups. Mucociliary clearance rates in terms of retention ratio after 1 hour and radioactivity half-life for each lung was lowest in the water-pipe smokers compared to others. Mucociliary clearance rate also decreased in the cigarette smokers compared to passive smokers. The differences in the mucociliary clearance rates among groups were statistically significant (p < 0.05). Urinary cotinine levels were highest in the cigarette smokers and higher in water-pipe smokers compared to passive smokers as statistically significant. As a conclusion mucociliary clearance rates decrease with tobacco smoking, being more prominent in water-pipe smokers in our study.