Mr Gul said the vote amounted to "domestic political games"
Turkey has denounced a vote by a US congressional committee describing as genocide the 1915-17 mass killings of Armenians by Ottoman Turks.
President Abdullah Gul said the decision was unacceptable and had no validity for Turkey, which has always denied any genocide took place.
The White House said it was very disappointed by the non-binding vote.
It fears Turkey could now limit co-operation in the war on terror and provision of military bases near Iraq.
The genocide bill passed in the House Foreign Affairs Committee by 27 votes to 21 - the first step towards holding a vote in the House of Representatives.
Divisions within the committee crossed party lines with eight Democrats voting against the measure and eight Republicans voting for it.
President Bush had argued against a vote in favour of the bill, saying "its passage would do great harm to our relations with a key ally in Nato and in the global war on terror".
Turkey is a regional operational hub for the US military, and some suggest access to Incirlik airbase, or other supply lines crucial to US forces in Iraq and Afghanistan, could be cut in response.
The influential Armenian diaspora in the US has lobbied for years for a recognition of the 1915-17 killings as genocide.
At least 20 countries at various levels of legislation have passed resolutions on this issue.
The Armenian President, Robert Kocharyan, welcomed the move by the US congressional committee, saying: "The recognition of historical injustice cannot harm bilateral relations."
President Gul was quick to attack the vote late on Wednesday evening, saying that some US politicians had "closed their ears to calls to be reasonable and once again sought to sacrifice big problems for small domestic political games".
"This unacceptable decision of the committee, like similar ones in the past, is not regarded by the Turkish people as valid or of any value," Mr Gul said, according to the Anatolian news agency.
The BBC's Sarah Rainsford in Istanbul says it is very unusual to hear such high-level political reaction so late at night - a sign of how seriously it takes this.
Meanwhile in Washington the US Undersecretary of State, Nicholas Burns, told the BBC that the Bush administration was "deeply disappointed".
"The United States recognises the immense suffering of the Armenian people due to mass killings and forced deportations at the end of the Ottoman Empire," he said.
"We support a full and fair accounting of the atrocities that befell as many as 1.5m Armenians during World War I, which House Resolution 106 does not do."
Correspondents say the committee's vote means that only a change of heart by the opposition Democrats, who control Congress, can now stop a full vote on the bill.
Tom Lantos, the committee's chairman, had opened the debate by admitting the resolution posed a "sobering" choice.
A German soldier took photos of Armenian deportees at the time
"We have to weigh the desire to express our solidarity with the Armenian people... against the risk that it could cause young men and women in the uniform of the United States armed services to pay an even heavier price than they are currently paying," he said.
Mr Lantos, a survivor of the Jewish Holocaust, said he would introduce a resolution praising US-Turkish friendship next week, according to AFP news agency.
The Senate Foreign Relations Committee is expected to take up their version of the resolution in the future.
The controversy comes at a delicate time for relations between Turkey and the United States, our correspondent says.
Prime Minister Recep Tayyip Erdogan has confirmed that the Turkish parliament will discuss a motion that would authorise cross border military incursions into northern Iraq to hunt down Kurdish PKK separatists.
He had said it could be discussed as early as Thursday, but it is now thought it will not be submitted to the house until next week, AFP news agency said.
The move comes after an escalation in attacks by the PKK killed almost 30 soldiers and civilians in just over a week.
Mr Erdogan said such authorisation, which would be valid for one year, would ensure all options were available to Turkey in its fight against the PKK.
That includes sending troops into northern Iraq, where the prime minister said more than 3,000 PKK fighters are based. The government is under immense pressure though to act, but Washington has warned Ankara against any unilateral moves that would destabilise Iraq even further.
After the Armenian vote in Congress, our correspondent says, Turkey will be far less inclined to heed instructions from the US on anything.