In the new center women will be treated by female specialists, who will wear headscarves or hijabs, while men will be examined by male medical staff.
The facility also includes a Halal cafeteria and a prayer room with a screen separating men from women, a buffet with non-alcoholic drinks and a drug store with only alcohol-free medicines.
The head of the Russian Mufti Council, Ravil Gainutdin, said the center will contribute to mutual understanding between nations and religions.
"In a multinational Russia each citizen has the right for the kind of treatment that fits their traditions," Gainutdin said.
Later such clinics are planned to be opened in the Republic of Tatarstan and Saratov.
Islam is the second largest religion in Russia, with Muslims representing some 15% of the population of 142 million.
