"Regarding NATO, let me say very clearly: Ukraine is a sovereign and independent country that has the right to choose your own alliances," she told Ukrainian Foreign Minister Kostyantyn Gryshchenko.
"NATO'S door remains open but it is up to Ukraine to decide whether or not you wish to pursue that or any other course for your own security interests," she added.
President Viktor Yanukovich, elected last February ousting a pro-Western leadership, has abandoned the aim of joining the US-led military alliance pursued by his predecessor, Viktor Yushchenko.
Clinton also expressed the hope Ukraine would reach a deal to secure a new multi-billion-dollar IMF loan and encouraged the country to strengthen its investment climate by economic reforms and protecting intellectual property rights.
"We know that you are undertaking reform plans, which we very much welcome. We hope that Ukraine will conclude an agreement with the IMF shortly to advance this process," she said.
An IMF mission is in Kiev for what the government hopes will be conclusive talks on a loan of up to $19 billion to boost Ukraine's economic recovery.
The Yanukovich leadership will be pleased to have Washington's blessing for what he says is a pragmatic policy that looks both to Russia and the West, and for Ukraine's efforts to stabilise its economy with help from global financial lenders.
Clinton's visit to Ukraine, the first stop on a five-country regional tour, is the highest-level US visit since he was elected and takes place after a flurry of pro-Russian moves by the new leadership.
Apart from downgrading contacts with the US-led military alliance, Yanukovich has tilted Ukraine firmly toward Moscow by extending the stay of the Russian navy in a Ukrainian Black Sea port and stepping up commercial contacts.
COMMITMENT TO DEMOCRACY
Unlike ex-Soviet Georgia, which Clinton will also visit, the Yanukovich leadership sees little danger in US President Barack Obama's new strategy of "resetting" relations with Russia.
Washington applauded in April Yanukovich's move to get rid of highly enriched uranium and has reacted publicly with some indifference to his downgrading of relations with NATO.
At the same time, however, analysts expect Clinton to make clear during her visit that Washington remains interested in Ukraine's direction under Yanukovich and its commitment to democracy.
Clinton was due to meet later with Yanukovich himself and late on Friday also see former Prime Minister Yulia Tymoshenko, Yanukovich's arch-rival who is now in opposition and under the shadow of possible prosecution for alleged misdemeanours while in office.
Analysts expect Clinton to press Yanukovich to ensure that there are no infringements of media freedoms and freedom of assembly in Ukraine. Last week, US Ambassador to Kiev John Tefft expressed concern about reports of pressure on journalists since Yanukovich came to power.
"We are also encouraged by your government's commitment to support freedom of the press and to take concrete steps to ensure the independence of Ukraine's vibrant media," Clinton told Gryshchenko.
Clinton stops in Krakow, Poland, on Saturday for a gathering of the Community of Democracies, a group that promotes democratic norms, and then visits Azerbaijan and Armenia, which have long sparred over Azerbaijan's breakaway Nagorno-Karabakh region.
