Here are some of the key things we learned.
Comey said the FBI was "investigating the nature of any links between individuals associated with the Trump campaign and the Russian government, and whether there was any coordination between the campaign and Russia's efforts".
He added that investigators believed Russian officials saw the possibility early on that Trump could win the election.
The congressional hearings were the most extensive public accounting of a matter that has dogged the Trump administration for its first two month.
Mr Comey said: "I have no confirmation that supports those tweets, and we have looked carefully inside the Federal Bureau of Investigation".
Both Manafort and Flynn are among the Trump associates under scrutiny for possible contacts with Russian Federation during the election.
Comey then contradicted several statements by the White House, including the president's incendiary claim that former President Obama had "tapped" Trump's phone.
"Yes. I understood the question to be about the report itself", Comey said.
"The unclassified intelligence assessment doesn't discuss the issue of United States person coordination with the Russians", Schiff said. Before Comey was sworn in at the hearing, Trump tried to set the tone with a series of early-morning tweets decrying the accusations of collusion with Russian Federation as "FAKE NEWS" being pushed by defeated Democrats and arguing that the real scandal is the leaking of sensitive information from within the intelligence community.
The part of this spectacle that matters the most is the part Comey is focused on: whether Russian attempts to help defeat Hillary Clinton involved collusion with anyone associated with Trump's campaign.
"Is it possible that all of these events and reports are completely unrelated and nothing more than an entirely unhappy coincidence? Yes, it is possible", said Schiff in his opening remarks.
Flynn resigned after a brief stint as Trump's national security adviser and has since retroactively registered as a foreign agent for his work representing Turkish interests; Democrats revealed on Friday that Flynn had also taken more than $50,000 in payments from Russian government entities.
"Let me be clear: We know there was not a physical wiretap on Trump Tower".
In keeping with FBI policy, Comey said he was not able to publicly comment on specific parts of the investigation.
Comey and the director of the National Security Agency (NSA), appearing before a congressional committee, stated that their probe into the Moscow links could go on for months. Comey replied, "We would have sent up a much larger flare, we'd have kept banging and banging on the door". This bothers me, because I feel my judgments on the world and the people in it can be too harsh.
So unlike Adam Schiff, who prosecuted the case for the Dems ruthlessly, the Republicans dithered, striking Comey with the flat of the blade.
Rogers said there were 20 people at NSA, including himself, who could do so.
"I have no information that supports those tweets", Comey replied to one of Schiff's leading questions.
Trump did tweet in 2012, "I don't mind that @BarackObama plays a lot of golf".
But Comey said the White House could only make such a request to the agency that collected the information. Then two days before the election he said the investigation, which probed disgraced ex-Rep. Some of them say that the FBI is investigating "campaign associates", but others say that the FBI is investigating "Trump".
In August, longtime conservative political operative and close Trump confidant Roger Stone said that he was in touch with WikiLeaks, the source through which Russian Federation released the hacked emails to the public.
The U.S. intelligence community concluded that Russian President Vladimir Putin ordered the hacking into computers at the DNC. Another tweet incorrectly said Comey and Rogers told lawmakers that Russian Federation "did not influence" the electoral process.
But Comey and Rogers had both pointedly refused to comment on the question.
At the hearing, the intelligence heads denied Donald TrumpDonald TrumpLawmakers want Trump commitment to help Iraq post-ISIS Tillerson to skip North Atlantic Treaty Organisation meet, visit Russian Federation: report Trump hits Colin Kaepernick at Kentucky rally MORE's repeated claim that he had been wiretapped and committed to help find the leakers. Suspicion fell on Russia nearly immediately, given Trump's pro-Russian approach to foreign policy and Russia's long history of interfering in Western elections.