That might appear to be an odd choice of destination following Yushchenko's inauguration speech yesterday. Kyiv's new leader never mentioned Russia and stated that Ukraine would seek European integration.
"Our path to the future is the path that united Europe is undertaking," Yushchenko said. "We, with the [European] nations, belong to the same civilization. We share the same values. History, economic perspective [and] the interests of our people give us a clear answer to the question: Where is our destiny? Our place is in the European Union and my goal is 'Ukraine in a United Europe.'"
Reacting today, Russian Foreign Ministry spokesman Aleksandr Yakovenko insisted that relations between the two countries would remain strong.
"Relations between Ukraine and Russia are defined by our history, geography, economy and ultimately by the destinies of our people," Yakovenko said. "There is no other way but to develop these relations. Of course, the development of our relations is based, first and foremost, on the national interests of our two peoples and our two countries."
Yet not all appears so clear-cut in Kyiv. Yushchenko, in his speech, also stressed Ukraine would pursue an independent national policy.
"Ukrainians will occupy their rightful place in the community of nations," Yushchenko said. "Ukraine will be neither a buffer zone, nor a playing field for somebody else's competition. We are ready to respect the interests of other nations. But for me, as it is for you, the national interests of Ukraine are above all."
The Kremlin, however, has different ideas.
Last week, Putin congratulated Yushchenko, emphasizing the "particular significance of Russia and Ukraine continuing their active participation in forming the Single Economic Space."
Oleksandr Sushko is director of the Center for Peace, Conversion, and Foreign Policy, a Kyiv-based think tank. He said that Yushchenko's visit to Moscow does not mean Yushchenko supports the Kremlin's integrationist plans.
Rather, Sushko said it is a bid to normalize relations that were strained during the presidential campaign, when Putin backed Yushchenko's rival, former Prime Minister Viktor Yanukovych.
"The visit takes place to a country with which relations have become strained during the last months," Sushko said. "It happened because of Russia's attitude toward the [Ukrainian] elections."
In November, Putin backed Yanukovych, whose apparent victory was marred by fraud and later annulled. Putin also congratulated Yanukovych on winning without waiting for the final results, angering Yushchenko's supporters.
But Yushchenko's visit to Moscow also reflects Ukraine's real interests. The country has deep economic ties to Moscow as well as a sizable pro-Russian minority. Yushchenko promised them he would normalize relations with Moscow.
Indeed, it is unclear how far can Ukraine distance itself from Russia without overly harming its relations with the Kremlin. For his part, Sushko said he believes Yushchenko has a lot of room to act.
"The Kremlin's displeasure we have already seen during the presidential campaign and the Ukrainian nation has made its choice and not the choice the Kremlin wanted," Sushko said. "Yushchenko has a pretty good carte blanche to pursue an independent policy of Ukraine toward Russia."
Sushko said that in the future, Kyiv will not be a satellite of Russia's as it was during the rule of former President Leonid Kuchma. However, it is unlikely that Ukrainian policy toward Russia will be confrontational, he added.
Kirill Koktysh of the Moscow Institute of International Relations said that Yushchenko's attitudes have never been anti-Russian and that his conflict was only with the Kremlin.
"Yushchenko never had nationalistic attitudes, as some believe," Koktysh said. "His attitudes are national but not nationalistic and here we have very subtle dividing lines. It is wrong to understand Yushchenko's victory as a victory of radically [nationalistic] western [part of Ukraine]."
He said that economic interests of Ukraine are in Russia and that many Russian businessmen supported Ysuhchenko's campaign because they would like to see a liberal and democratic ruler different from the one they have at home.
As for possible Ukrainian integration into Europe, Koktysh said that may be too ambitious for now. Not just because of Ukraine's close ties with Russia. European integration also requires painful economic reforms -- and Ukraine may not yet be ready for them.
And forcing such reforms, Koktysh said, could hurt Yushchenko's political career.