As that dust settled, health officials and scientists sought to figure out what was in it, and what the health effects of it could be.
SLIDESHOW: What Was in the 9/11 Dust?
"The dust is something we had never seen before," said Paul Lioy, director of exposure science at Rutgers University and UMDNJ Robert Wood Johnson Medical School. "It was caused by the collapse and disintegration of two very large structures."
The federal government and the Port Authority of New York and New Jersey asked Lioy to collect and analyze samples of the dust and what the possible health consequences could be.
Analysis showed that the substances in the dust included cement, gypsum, asbestos, glass fibers, calcium carbonate, lead and other metal particles.
"The particle sizes are not what we normally see in the air every day -- these were very large, extremely large. We didn't even have a definition for the size," said Lioy, also the author of "Dust: The Inside Story of its Role in the September 11th Aftermath."
The pH of the dust was very high, meaning it was highly alkaline.
"That means it's extremely caustic and would be like inhaling powdered lye or Drano," said Dr. Philip Landrigan, dean for global health at the Mount Sinai School of Medicine in New York.
The toxicity of the dust had a significant impact on the health of many first responders who were present, and those effects were especially severe among people exposed to the dust on the first day and for an extended period of time.
Research done at Mount Sinai in 2009 found that about eight percent of men and women who helped with rescue and recovery, or took part in other work at the site, reported asthma attacks. Normally, only about four percent of the population suffers from asthma.
The New York City Department of Health said asthma risk was also increased for people who lived and worked in lower Manhattan after 9/11.
"A lot of the respiratory diseases and the gastroesophageal reflux disease (GERD) we're seeing in the 9/11 responders is the direct consequence of inhaling this toxic dust," said Landrigan. "It lands in the sinuses and bronchial tubes, causing irritation, redness and swelling." The dust's alkalinity is believed to be the cause of the "World Trade Center cough."
Over time, this redness and irritation goes away but is replaced by scar tissue, and if the amount of scar tissue is extensive, it can lead to chronic lung disease.
Lead and other heavy metals can be toxic to the brain, and gypsum, a component of drywall, can cause respiratory problems if it's inhaled over a prolonged period of time. But Landrigan said two of the substances -- cement dust and asbestos -- are the most harmful.
Cement dust made up about two thirds of the overall dust, which contributed to its high alkalinity. The effects of asbestos wouldn't be felt right away, but could become evident in the next few years.
"Asbestos is a human carcinogen," Landrigan explained. "It causes lung cancer, laryngeal cancers and malignant mesothelioma, and these typically develop anywhere from 10 to 30 years after exposure."
While the dust was highly toxic, Lioy said it's impossible to say which specific substances contributed to the health problems since it was a mixture of things and the effects of gases couldn't be taken into account.
"The gases were released very quickly and then went away, so it's impossible to determine what could have been there."
Normally, the body is able to filter out certain substances, but the dust that fell from the towers overcame the body's defenses.
"The concentration of toxic materials was so high that when those people took a breath, the junk in the air overwhelmed the normal mechanisms we have in our nose and throat," said Landrigan.
In January, President Obama signed into law the James Zadroga 9/11 Health and Compensation Act, named in honor of a New York City police officer whose death was linked to dust exposure. The bill set aside money to provide health monitoring, treatment and compensation to affected workers.