People who inhaled the sweet-smelling fumes of 'hookah' smoke were more likely to gain weight and develop type 2 diabetes in comparison to those who didn't.
Cigarette smoking was not linked to obesity, metabolic syndrome, dyslipidemia or diabetes, the research also uncovered.
The negative effects are said to be the equivalent or worse than smoking a pack of cigarettes, experts at the Brighton and Sussex Medical School warned.
The results of the study, which involved academics at a university in Iran, were published in Diabetology and Metabolic Syndrome.
Shisha is a leisure activity, hailing from the Middle East. It is often considered to be a more 'healthy' alternative to smoking.
But while shisha may not contain many of the carcinogenic additives in cigarettes, mounting evidence suggests the water pipe tobacco is still not safe.
The research involved 9,840 participants - a mixture of smokers, non-smokers, ex-smokers, cigarette smokers and hookah smokers.
The participants, from Iran, took a questionnaire which investigated their smoking history, cardiovascular risk factors and anxiety and depression.
This was then measured against their biochemical results, analysed by taking blood tests.
'Obesity, metabolic syndrome, diabetes and dyslipidemia were positively associated with hookah smoking while negatively associated with cigarette smoking,' the authors wrote.
'In contrast with the public belief that hookah eliminates the toxicity of tobacco in comparison with cigarettes, we found that the adverse effects of hookah smoking could be even greater than cigarette.'
Professor Gordon Ferns, of Brighton and Sussex Medical School, told The Telegraph: 'A single session of hookah smoking may be equivalent to more than a packet of cigarettes, and the inhaled toxic compounds may be even greater.
'It is unclear why hookah smoking is associated with obesity and diabetes.
'It is possible that the toxins in the smoke stimulate an inflammatory response that causes tissues to become resistant to the effects of the hormone insulin, that regulates glucose in the blood.
'However, it is also possible that hookah smoking is associated with other social behaviours that lead to weight gain.
'There is now good evidence that hookah smoking is not harmless. The risks of hookah smoking with respect to some types of cancer is well established, and the evidence for an association with cardiovascular disease is growing.'
The ancient form of smoking, also called narghile, waterpipe, or hubble bubble smoking, uses charcoal-heated tobacco or non-tobacco based shisha smoke which is passed through water before inhalation.
It is often seen as less toxic compared to cigarettes, alongside e-cigarettes and vaping.
The sweet flavours available make shisha smoking desirable, especially the young people - around half of smoking that teenagers do are is in this way.
Hookah smokers can spend long periods of time in lounges and bars inhaling the fumes.
A typical hookah session lasting one hour involves 200 puffs, which results in 90,000 milliliters of smoke being inhaled.
Smoking a cigarette involves 20 puffs, resulting in 500 – 600 milliliters of smoke being inhaled, according to the Centers for Disease Control and Prevention.
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