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This comes after a report found that they are just as damaging to a person's health as manufactured cigarettes.
Research by public health officials found that male smokers using hand-rolled cigarettes had more than doubled from 18% in 1990 to 40% in 2013. While women smoking roll-ups went from just 2% to 23% in the same period.
The figures were highlighted ahead of a new hard-hitting campaign by Public Health England (PHE) warning smokers of the damage caused by their habit.
Professor Dame Sally Davies, the chief medical officer, said: "Significant numbers of smokers are now using roll-ups without realising that gram for gram of tobacco they are just as unsafe as ordinary cigarettes.
"The research we have got suggests that people think it's safer to smoke a roll-up up but they are wrong, it is not safe.
"No tobacco is safe and gram for gram it is as harmful as ordinary cigarettes."
PHE's new digital campaign and billboard ads remind smokers of the damage done by cigarettes to the brain, bones and muscles, teeth and eyes.
Current smokers are 59% more likely to develop Alzheimer's disease and have 53% more probabilities of suffering cognitive impairment, according to PHE.
They also heal slower and have increased risk of back and neck pain, with a 79% increase in chronic back pain and 114% increase in disabling lower back pain.
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In terms of harm to bones, smokers have a 25% increased risk of fracture and a 40% increase in their probability of breaking a hip.
Damage to the eyes includes an increased risk of age-related macular degeneration of 78% to 358%, and also an increased likelihood of age-related cataracts.
"This is our third hard-hitting campaign. The first was about cancer, the second was about heart attacks and strokes, and this one is about the general rot that tobacco does to your body," Davies said.
"We have evaluated the other two campaigns and they have had real impact on the public and that has then fed through into orders for quit kits and people stopping smoking."
Although smoking rates have declined to an all time low this year of 18.4%, the habit is still the biggest cause of preventable illness and premature death in the country, with almost 80,000 people dying in England a year.
One in every two long-term smokers will die prematurely from a smoking-related disease unless they quit.
The new campaign by PHE features a graphic anti-smoking advert, showing a father lighting a hand-rolled cigarette full of rotting flesh.
Dame Sally Davies said: "Whilst many smokers know the damage cigarettes do to their hearts and lungs, they are much less likely to be aware of how harmful smoking is to the body - essentially 'rotting' it from the inside out, and roll-ups are no exception.
"January is a time when many people make New Year's resolutions to improve their health and try to stop smoking.
"Millions of people have used Smokefree support and we are hoping that this year, even more will take advantage of the free expertise and resources on offer," she added.
Meanwhile, smokers' rights group Forest has labeled the campaign as "poisonous".
Chief executive of the group, Simon Clark told the Daily Mail: "There can't be a sane adult in the United Kingdom who isn't well aware of the health risks of smoking."
"What's really poisonous is the way public health campaigners are constantly trying to scare and harass people with exaggerated claims and dubious statistics."
"Campaigns like this are an abuse of public money," he added. "Education has been replaced by shrill scaremongering that is often counter-productive."
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