"What you see is a lot of fingerprints in terms of the tactics and techniques and procedures that are being employed. We are working very hard to establish whether there are today positive links," Lieutenant-General Ricardo Sanchez said in an interview.
"We believe that those links may be growing."
Sanchez said the devastating car bombings against Western troops had raised fears al-Qaida had a hand in the bloodshed.
"It is the frequency of the attacks and the types of attacks that are being conducted. You have Nasariya, you have Karbala, quite complex attacks with car bombs," he said.
"Those are typically tactics al-Qaida has been using. That causes us to look with a little bit more focus, trying to establish what their operating capability is in the country."
Violence has gripped Iraq since US-led occupation forces toppled Saddam in April.
Insurgents have killed 240 American soldiers since major combat was declared over on 1 May.
On Sunday, an improvised bomb exploded close to a hotel in the centre of Baghdad as a US occupation military convoy was driving past, a US soldier on the scene said.
The bomb, which was concealed in a rubbish heap close to the Masbah hotel in the upmarket Karrada district, exploded around 0730 GMT, but there were no immediate reports of casualties.
One US soldier on Sunday died of
wounds suffered in explosion
Also on Sunday, a US occupation soldier died from wounds he suffered when fighters fired a rocket-propelled grenade at his armoured vehicle, the US Army said.
A spokeswoman for the US 4th Infantry Division, Major Josslyn Aberle, said the attack occurred on Saturday night near the town of Baiji, north of the Iraqi capital.
Lethal bombings against the United Nations and US-backed Iraqi police, as well as grenade and roadside bomb attacks on US troops, have fuelled suspicions that foreign fighters have joined forces with Iraqi insurgents.
Such an alliance would be a new one. The secular nature of Saddam's Iraq ran counter to the views of groups like Usama bin Ladin's al-Qaida.
US military officials say foreign fighters have crossed over the Syrian border into Iraq.
"There are some. We are still finding them and killing them here in the country. We know they are operating in small numbers here in the country. That continues at a steady pace"
Lieutenant-General Ricardo Sanchez,
US military commander in Iraq
"There are some. We are still finding them and killing them here in the country. We know they are operating in small numbers here in the country. That continues at a steady pace," said Sanchez.
Speaking after bombings killed six US soldiers over the weekend, he said he was concentrating on "a terrorist extremist element that may be beginning to get a foothold" in Iraq.
"That's what we have to work very hard to eliminate," he added.
Asked if he thought Iraq was stable enough to handle a power handover, Sanchez said engagements with guerrillas had eased off.
"When you are talking about less than 20 engagements across this entire country on any given day, that's the average that we are experiencing right now. We are focused on providing a security that will be necessary to have either the caucus method or elections," he said.
"We will be working very hard with the Coalition Provisional Authority and the Iraqi people to make sure that security is there for this democratic process to evolve."