Sufferers of the agonising digestive disorder avoid eating the protein as it can make them severely ill.
However, it is believed about 13 per cent of the UK population have started to avoid the protein by choosing such products instead. And the figure is even higher in the US, with a quarter saying they had consumed such foods in 2015 - a 67 per cent increase in two years.
Gluten-free versions of bread, spaghetti and cereals often contain rice flour as a substitute for wheat.
But rice is known to contain up to ten times more arsenic than other foods because of the way it is grown.
Generally, brown rice has higher levels because the arsenic is in the outer coating or bran, which is removed in the milling process to produce white rice.
Industrial contaminants and pesticides can remain in the polluted paddy fields for decades - meaning the rice in supermarket shelves often contains higher levels.
Researchers from the University of Illinois at Chicago assessed the urine of 73 participants, aged between 6 and 80, from a previous nutrition survey who had all reported eating gluten-free food over five years.
However, those who consumed the most rice-based substitutes had higher concentrations of arsenic in their urine, they found.
Their levels of the toxic metals were almost twice as high, according to the study published in the journal Epidemiology.
Traces of mercury were almost 70 per cent greater in those restricted to a gluten-free diet.
Study author Dr Maria Argos said: "These results indicate that there could be unintended consequences of eating a gluten-free diet."
However, she added that further research is needed to determine the health effects of consuming the metals.
