The US missile shield plans have strained relations between the two countries.
Washington describes its proposal to station interceptor missiles in Poland and a targeting radar in the Czech Republic by 2012 as a safeguard against the threat of a missile attack from states such as Iran.
Moscow sees the plan as a step towards weakening Russian security, but has offered access to a Russian-controlled early warning radar in Azerbaijan as an alternative.
Putin also used the talks to warn that Russia could withdraw from a Cold War-era treaty that limits its missile stockpiles, unless the agreement was enlarged to include other countries.
Putin did not specify the particular treaty, but appeared to be referring to the Intermediate-Range Nuclear Forces Treaty signed between the two countries in 1987.
The Russian leader has also threatened to suspend Russian adherence to another arms control treaty, known as the Conventional Forces in Europe pact.
Gates said the two-day, closed-door talks would cover "an ambitious agenda for security issues that concern both of us", though he did not directly comment on the missile defence dispute.
The two powers are due to examine a range of issues on which Russia and the US differ, including the status of Kosovo and Iran's nuclear programme.
Putin said on Wednesday that he saw no evidence Iran was hiding a bomb-making project behind the largely Russian-built civilian nuclear power programme.
But Rice, who hopes to persuade the Kremlin to back stronger action against Tehran, said en route to Moscow that she believed the Russians were worried by Iran's intentions.
A Russian proposal to handle Iran's uranium processing on Russian territory and to control any spent fuel revealed "suspicion about Iran's intentions", she said.