He died at the Victoria Infirmary in Glasgow yesterday. NHS Greater Glasgow and Clyde said blood tests had shown the presence of the deadly bacteria.
Health officials said another heroin user being treated at the same hospital has also tested positive for anthrax. And a third patient, who is being treated at Glasgow Royal Infirmary, is being tested for anthrax. All three had infections in areas of the body they injected with heroin.
The health board confirmed that the dead drug user was male as is the patient at the Royal Infirmary, while the patient at the Victoria Hospital is a woman.
It is not known if the three cases are directly linked.
The victim is believed to have died from the anthrax infection.
Consultant epidemiologist Dr Colin Ramsay, of Health Protection Scotland, told a press conference in Glasgow: "The evidence is that heroin is prepared in non-sterile circumstances and therefore it is conceivable it could be contaminated by a variety of organisms which could happen naturally if they occur in the environment in which the heroin is prepared.
"We are not suggesting that there is any evidence that someone deliberately added it.
"I think the evidence is that heroin comes from countries where anthrax is more likely in the animal population so the chances of it being in the environment in these countries is higher.
"It's highly conceivable that it could have been contaminated either from the source in the origin country or it could have been contaminated as a consequence of subsequent cutting when it arrived in this country."
Dr Ahmed said: "One of the possibilities is that this bonemeal is used, bonemeal being produced from animals, that could be one of the sources but this is speculation.
"We have no way of knowing how it might have got contaminated."
The outbreak team dealing with the infection will meet again tomorrow to discuss the situation, the health board said.
NHS Greater Glasgow and Clyde said its Public Health Protection Unit was now working with the Procurator Fiscal and Strathclyde Police to identify the source of the anthrax.
One possibility being investigated is that contaminated heroin, or an agent used to cut the drug, may be to blame.
Dr Syed Ahmed, consultant in public health medicine, said the risk to the general public was "negligible".
He said: "I urge all drug-injecting heroin users to be extremely alert and to seek urgent medical advice if they experience an infection.
"While this section of the community need to be on their guard, the risk to the rest of the population, including close family members of the infected cases, is negligible.
"It is extremely rare for anthrax to be spread from person to person and there is no significant risk of airborne transmission from one person to another."
Any heroin users admitted to hospital with serious soft-tissue infections now or during the last four weeks will now be investigated for anthrax.
Anthrax was suspected of being responsible for a spate of deaths among Scottish heroin addicts in 2000.
New Scientist magazine reported that tests at the UK biological defence lab in Porton Down found signs of infection in dead addicts.
But health officials in Glasgow, where several of the deaths took place, insisted at the time that the drug users were not infected by anthrax.
The last two known anthrax-related deaths in Britain were both of men who made drums.
In 2006 Christopher Norris, 50, from Stobs, near Hawick, died after inhaling anthrax.
Mr Norris made artworks and musical instruments, including drums.
A report from NHS Borders said Mr Norris is likely to have caught the disease after playing or handling anthrax-contaminated West African drums at a drumming workshop.
Last November, drum-maker Fernando Gomez, who is thought to have inhaled anthrax spores while handling imported animal skins, died in hospital in London.
The 35-year-old Spanish folk musician had been in the intensive care unit for several days.
Five people died and 17 others were ill in a series of anthrax attacks in the US in 2001.
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