Hookah is thought to be "less dangerous" than cigarettes because it forces the smoke to go through water before it reaches the lungs.
Most physicians believe it filters out the harmful toxins.
But researchers from Iran, headed by Dr Mohammad Hossein Boskabady found that water pipe smoking and deep inhalation cigarette smoking had the same effects on respiratory system, 'The Jerusalem Post' reported.
"Our findings reveal that there were profound effects of water pipe smoking on lung function values, which were similar to the effects observed in deep inhalation cigarette smokers," researchers were quoted as saying by the paper.
The study compared lung function and respiratory symptoms among water pipe smokers, deep- or normal-inhalation cigarette smokers and nonsmokers.
Three groups of smokers, including 57 water pipe smokers, 30 deep inhalation cigarette smokers and 51 normal inhalation cigarette smokers were identified and studied.
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In addition, 44 non-smokers were studied as a control group.
Results showed an increased prevalence and severity of respiratory symptoms among water pipe smokers and cigarette smokers.
Similar effects of water pipe smoking and deep inhalation cigarette smoking on respiratory status were found.
A quarter to a third of water pipe smokers suffered from wheezing, while almost 37 per cent had chest tightness and 21 per cent had a cough.
"Our study is the first report regarding the importance of the method of cigarette smoke inhalation with respect to effects on the respiratory system," Boskabady said.