Serbia has warned Croatia about the impact on diplomatic ties
Croatia and Hungary - two of Serbia's neighbours - have officially recognised Kosovo's independence.
A similar move is expected on Thursday by Bulgaria, another Balkan nation.
Serbia's foreign minister said Kosovo was "an illegal state", warning that nations that had recognised it "cannot count on good relations with us".
Separately, UN police began returning to the Serb part of the Kosovo town of Mitrovica, after clashes there in which a UN officer was killed on Monday.
The police left the northern part of the town after fighting pitched battles with Kosovo Serbs who had earlier seized a city courthouse.
A UN policeman from Ukraine was fatally wounded during the clashes, and more than 130 people - both protesters and international forces - were wounded.
'Difficult to swallow'
On Wednesday, Croatia and Hungary officially announced that they had recognised Kosovo as an independent state.
"The government has accepted the decision of the Kosovo parliament on declaring the independence of Kosovo on 17 February," a statement by the government in Zagreb said.
Croatian Prime Minister Ivo Sanader told reporters he realised that the decision "is a difficult one for Serbia to swallow".
"But I don't expect a worsening of political and economic relations because there is no alternative to good neighbourly relations," Mr Sanader said.
Croatia's Deputy Prime Minister Slobodan Uzelac, an ethnic Serb, immediately tendered his resignation in protest against the move.
Croatia is the second former Yugoslav republic to recognise Kosovo, after Slovenia.
In Budapest, the foreign ministry said that, in common with the majority of EU and Nato member states, Hungary had decided that "internationally supervised independence may offer the best way out of the crisis".
The Bulgarian foreign ministry said Sofia would officially recognise Kosovo on Thursday.
The announcements came shortly after Bulgaria, Croatia and Hungary said in a joint statement that they intended to recognise the authorities in Pristina.
The statement described Kosovo's case as unique and also made it clear that Bulgaria, Croatia and Hungary would support EU and Nato efforts to build democracy in Kosovo.
The document also expressed hopes that Belgrade would keep "its European orientation".
Hungary and Bulgaria are both part of the 27-member EU, and Croatia is negotiating EU membership.
On Wednesday, Serbian Foreign Minister Vuk Jeremic urged Belgrade's neighbours not to recognise Kosovo, warning that there would be consequences.
"I call on states, particularly those of the region, not to take this step. Do not injure our country's territorial integrity and sovereignty," he said.
Serbian President Boris Tadic had already warned Croatia that recognising Kosovo would have an immediate negative impact on relations.
Croatia's own declaration of independence in 1991 prompted a four-year conflict with Serb-led Yugoslavia.
Ties have steadily improved but Belgrade is likely to take diplomatic action.
Serbia has recalled its ambassadors from about 30 countries that have recognised Kosovo.
While most EU member states have already recognised Kosovo's independence, a significant minority - including Spain, Slovakia, Romania and Cyprus - have refused to accept the declaration.