Talks are expected to focus on international problems that concern both countries, including Iran's nuclear program and the future status of Kosovo.
Solving Problems Jointly
Merkel has stressed that Germany and Russia are "bound together by a strategic partnership," ahead of two days of talks with Putin.
The two leaders are to have a working dinner in the city of Wiesbaden on the banks of the Rhine River after Putin lands later today.
In a weekly video broadcast on October 13, Merkel said today's discussions will focus on problems they are jointly working on, including Iran's controversial nuclear program.
Putin has shown no sign of falling into line with the opinion of leading Western nations on how to deal with Tehran's defiance to meet international demands to halt sensitive nuclear work.
The two countries also disagree over Kosovo, with Russia denouncing Western support for independence for the ethnic Albanian-majority Serbian province.
Missile Shield On Agenda
Putin and Merkel are also expected to discuss the standoff between Moscow and Washington over U.S. plans for a missile shield in Eastern Europe. Merkel has insisted that NATO should be consulted about U.S. plans for the shield that would be based in Poland and the Czech Republic.
The agenda is also expected to touch upon energy security and economic issues, and Merkel is expected to raise human rights and political issues.
Putin's visit comes one day after U.S. Secretary of State Condoleezza Rice told representatives of Russia's civil society in Moscow that the United States wants to help Russia build strong institutions respectful of universal values.
"If Russia is to emerge as a democratic country that can fully protect the rights of its people, it is going to emerge over years and you have to be a part of helping the emergence of that Russia," she said. "The United States, of course, wants to be a partner in the emergence of a democratic Russia."
Rice: Kremlin Too Powerful
Rice later told journalists that she thinks "there is too much concentration of power in the Kremlin.... Everybody has doubts about the full independence of the judiciary."
She continued: "There are clearly questions about he independence of the electronic media and there are, I think, questions about the strength of the Duma."
In Moscow on October 12, talks between the foreign and defense ministers of Russia and the United States failed to reach agreement on the planned U.S. missile shield.
Russia also reaffirmed it will not back new sanctions against Iran over its nuclear program.
Speaking in Wiesbaden on October 13 at the start of the annual St. Petersburg Dialogue between Germany and Russia, former Soviet leader Mikhail Gorbachev regretted what he saw as "mistrust" in the European Union towards Russia.
Putin and former Chancellor Gerhard Schroeder initiated the annual St. Petersburg Dialogue as part of the German-Russian Forum in 2001.