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Cigarette smoking has been shown to be associated with changes in coagulation factors in the circulation and the subsequent thrombosis development. In this study, the impact of waterpipe smoking on the levels of fibrinogen, factor VII (FVII), and factor VIII (FVIII) was investigated. In addition, the effects of waterpipe smoking were compared to those of cigarette smoking and never smokers. A total of 80 male smokers (40 cigarette smokers and 40 waterpipe smokers) and 40 apparently healthy never smokers were recruited in the study. Both waterpipe smoking and cigarette smoking induced significant increases in the plasma levels of fibrinogen, factor VII, and factor VIII (p < 0.01). The magnitude of the increase in fibrinogen levels induced by waterpipe smoking was higher than that induced by cigarette smoking (p < 0.01), while similar increases were observed in other factors (p > 0.05). In addition, in the waterpipe group, the magnitude of the increase in fibrinogen and factor VIII was higher in the smokers with more than 3 years of use (p < 0.05). In conclusion, similar to cigarette smoking, waterpipe smoking modulates the levels of coagulation factors, suggesting its thrombotic potential.