New research showed vaping can "compromise" the function of the immune system in the airways more than tobacco and flavourings were the worse.
More and more people are using electronic cigarettes under the assumption they are not as harmful for your health as traditional cigarettes.
The US Food and Drug Administration (FDA) classifies many liquid flavourings in e-cigarettes as "Generally Recognised as Safe."
Researchers from the University of North Carolina School of Medicine point out this classification is designated for oral consumption.
Yet most flavourings have not been tested for their effects on the respiratory system.
Professor Ilona Jaspers, who led the study, said: "The digestive systems and respiratory systems are very different.
"Our stomachs are full of acids and enzymes that break down food and deal with chemicals; this environment is very different than our respiratory systems.
"We simply don't know what effects, if any, e-cigarettes have on our lungs."
For the study, researchers examined tissue samples of the epithelial layer inside the nasal cavities of smokers, non-smokers, and users of e-cigarettes.
They looked for any changes in more than 600 genes involved in the function of immune responses.
They also looked at the nasal lavage fluid, urine, and blood samples of participants to study the changes in genetic and proteomic markers of tobacco and nicotine exposure, as well as other markers of inflammation or immune responses.
The result showed smoking cigarettes causes the suppression of several key immune genes in the nasal mucosa.
Yet e-cigarette users showed the same changes in those genes, and also demonstrated suppression of several additional immune genes, suggesting an even broader effect on the respiratory mucosal immune response system.
The researchers say these effects could be down to the flavouring of the e-cigarettes.
In another separate experiment, scientists at the same lab examined the effects of cinnamon-flavoured e-liquids and the chemical that makes an e-cigarette taste like cinnamon, called cinnamaldehyde.
Professor Jaspers said: "We found that cinnamaldehyde e-liquids have a significant negative effect on epithelial cell physiology.
"The chemicals compromise the immune function of key respiratory immune cells, such as macrophages, natural killer cells, and neutrophils."
This compromised function of the respiratory cells could be a sign of changes in cells which could lead to impaired immune responses in the lung.
Researchers hope will now look to find out if long-term exposure to e-cigarettes - especially those with cinnamon-flavoured e-liquids - has immune suppressive effects on the respiratory mucosa in smokers.
They said if they do have an effect then it would be a sign e-cigarettes are not as safe as believed and advertised.
The findings from the research will be presented at the American Association for the Advancement of Science (AAAS) annual meeting in Washington DC.