The United States Agency for International Development (USAID) has announced it will close its offices in Russia following an order from the authorities there to cease operations.
The Russian government gave the US until 1 October to close the mission, accusing it of meddling in politics.
USAID has worked in Russia for two decades, spending nearly $3bn (£1.8bn) on aid and democratic programmes.
The expulsion follows a government crackdown on pro-democracy groups.
"The decision was taken mainly because the work of the agency's officials far from always responded to the stated goals of development and humanitarian cooperation. We are talking about attempts to influence political processes through its grants," the foreign ministry said in a statement.
The Russian authorities have become increasingly suspicious of non-governmental organisations (NGOs), which it believes are using foreign funding to foment political unrest, says the BBC's Steve Rosenberg in Moscow.
The United States began its operations in Russia after the end of the Soviet Union, spending around $2.7bn (£1.7bn) on a wide range of human rights, civil society, health and environmental programmes.
Earlier this year, President Vladimir Putin alleged that protests surrounding his re-election were orchestrated by US-funded NGOs.
Among the groups likely to be affected is Golos, whose exposure of electoral fraud at last year's parliamentary elections helped spark huge anti-Kremlin street demonstrations.
Golos is partly funded by USAID.
US stays 'committed'
In announcing the closure of the USAID office, US state department spokesperson Victoria Nuland said: "We remain committed to supporting democracy, human rights, and the development of a more robust civil society in Russia and look forward to continuing our cooperation with Russian non-governmental organisations."
She would not be drawn on the reasons behind the Kremlin's decision, but said there was a sense "that they don't need this any more".
USAID was due to spend around $50m on its work in Russia this year.
Russian human rights activists lamented the decision to expel USAID.
The head of Golos, Liliya Shibanova called it "a bad signal", saying there were very few other sources of funding for election monitoring groups, and that she expected to see other NGOs leaving Russia.
The head of Moscow Helsinki Group, Lyudmila Alekseyeva, said it was the Russian population, rather than the US, which would suffer from the loss of "useful services... free legal consultations, educational programmes and others".
The episode is reminiscent of Russia's crackdown on the British Council, which sponsors educational programmes, in 2007, during Vladimir Putin's last term as president.
Following the row with Britain over the poisoning of Alexander Litvinenko in London, Moscow ordered the closure of the council's offices and launched a tax investigation. The council now has just one office in Russia, in Moscow.