The move comes after watchdog Rospotrebnadzor temporarily shut four McDonald’s restaurants in Moscow.
The actions come amid rising tensions and sanctions between Russia and the West over the crisis in the Ukraine.
The regulator denied the checks were politically motivated. McDonald’s said “top quality” food was its priority.
The regulatory agency said: “There are complaints about the quality and safety of the products in fast food restaurant chain McDonald’s.”
McDonald’s is one of the symbols of America.
Russian parliament has also called for checks on other US fast-food brands, including Burger King and KFC.
McDonald’s said its main priority was to serve customers “top quality menu items”, and that it was studying a claim by the food standards watchdog “to define what should be done to re-open the [Moscow] restaurants as soon as possible”.
Russian state news agency Ria Novosti reported that the regulator was preparing to take McDonald’s to court over alleged breaches of health and safety regulations.
McDonalds decline to comment on that report.
Unscheduled checks will be made in McDonald’s restaurants in the region of Sverdlovsk in west-central Russia, the Volga region of Tatarstan, the central Voronezh region, and the Moscow region.
“There has been a selection of microbiology tests, sanitary and chemical tests, and identification indicators,” the watchdog said.
McDonald’s said it was “open to any checks”.
A company spokeswoman for European operations said it was aware that the regulator was carrying out the checks, which would be likely to continue for a couple of months.
The spokeswoman added that McDonald’s serves millions of customers a day in Russia, and wanted minimal disruption for them.
According to Ria Novosti, checks have been ordered across Russia’s Central Federal District, and that inspections of McDonald’s in all of the country’s regions will take place.
The checks and restaurant closures come amid a background of diplomatic tensions and tit-for-tat sanctions between Russia and the West over the crisis in the Ukraine. The West has accused Russia of supporting pro-Russian militants.
Earlier this month, Russia imposed an embargo on food imports from the EU, US and some other Western countries, in response to sanctions over Ukraine.
On August 20, the regulator temporarily closed four Moscow restaurants as part of an ongoing investigation of McDonald’s.
The first ever McDonald’s in Pushkin Square, which opened in 1990, was one of the outlets that was shut. Restaurants on Manezh Square, Svobodny prospect 35b and Prospect Mira were also closed.
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