Researchers from Charles University, Prague took pictures of 80 men and women and asked almost 250 volunteers to rate them.
Overall, brown-eyed faces were judged to be more trustworthy than the blue-eyed ones and the women as more trustworthy than the men, the 'Daily Mail' reported.
Women with brown eyes marked pictures of blue-eyed females lower than those whose eyes were green or brown.
Those women with brown eyes rated brown-eyed female faces more highly than blue-eyed ones.
The colour of the eyes on the pictures were then changed, to see if this affected perceptions.
For male participants the change did not make a difference, suggesting there is something about the shape of brown-eyed faces that conveys honesty.
Photos of men with brown eyes tended to have bigger eyes, noses and broader chins.
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Smaller facial features may lead to a man being perceived as less masculine, and so less trustworthy, the researchers said.
Faces that were rated as attractive were also seen to be trustworthy, the study found.
The research was published in the journal PLoS ONE.