The findings suggested that e-cigarettes pose health risks despite being widely considered a safer alternative to tobacco cigarettes.
Researchers exposed frog embryos and samples of mammalian neural crest cells to saline infused with e-cigarette vapour.
Frogs, like other vertebrates, are similar to humans embryonically, said Amanda Dickinson, from the Virginia Commonwealth University (VCU) in the US.
"This means that if a chemical perturbs a frog embryo, it's likely to do the same thing to a human embryo," Dickinson said, one of the authors of the study published in the journal PLOS.
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Damage to these cells in utero can cause craniofacial birth defects, said Rene Olivares-Navarrete from the VCU.
"Neural crest cells are extremely important in the development of craniofacial structures because they can form many different tissues like bones, cartilage, skin, teeth and glands," Olivares-Navarrete said.
E-cigarettes are connected to the pump, which "inhales" the vapour.
Vapour is created when e-liquids - blends of nicotine, propylene, glycol, vegetable glycerin and various flavouring compounds - are heated within e-cigarettes during inhalation.
The vapour is then collected in a syringe before it is infused into saline.
They tested the effects of the mixture on the viability and function of neural crest cells.
The results were surprising and strongly suggested using e-cigarettes could lead to birth defects, Dickinson said.
In experimental trials for specific e-liquid types, all the frog embryos developed cleft palates.
"We observed that very complex e-liquids that mix flavors, such as berries and creme and other food-related flavourings, may have the most dramatic effect on the face," Dickinson said.