The release of 20,000 hacked emails, which showed the Democratic National Committee favoured Clinton during the primary contest with Bernie Sanders, has led to ugly scenes at the Democratic convention and resignation of the party chair.
In what should be a triumphant occasion for Clinton that confirms her as the Democratic nominee for the presidential race, her name has instead been greeted with loud boos and chants of "Bernie" from Sanders supporters at the convention.
The dissent is a gift for her Republican rival Donald Trump, who was officially endorsed as the presidential candidate by his party last week.
A cybersecurity firm the Democrats hired after they realised they had been hacked, found traces of at least two sophisticated hacking groups called "COZY BEAR" and "FANCY BEAR" on their network - both had ties to the Russian government.
Those hackers took at least a year's worth of detailed chats, emails and research on Trump, a person knowledgeable of the breach told AP.
Metadata associated with the file suggests that the documents passed through Russian computers. They were last saved by someone named (in Cyrillic letters) "Felix Edmundovich," a possible reference to "Iron Felix", a historical figure who was best known for establishing the Soviet secret police.
The release of the emails on Wikileaks just before the Democratic convention was designed to inflict maximum possible damage, but it also came just a week after Trump made troubling comments about US support of NATO.
Trump told the New York Times he would decide whether to protect America's NATO allies against Russian aggression based on whether those countries "have fulfilled their obligations to us". It follows earlier comments from Trump that praised Russian President Vladimir Putin as a strong leader, while criticising the 28-member NATO alliance as "obsolete and expensive", sparking fears from Eastern European countries like Lithuania that Trump will "kowtow" to Putin.
On Sunday, Clinton campaign manager Robby Mook said that it was "concerning last week that Trump changed the Republican platform to become what some experts would regard as pro-Russian."
Other links between Trump and Russia have also emerged.
The Washington Post revealed last month that Trump also relies heavily on Russian money.
"Russians make up a pretty disproportionate cross-section of a lot of our assets," Trump's son, Donald Junior reportedly said in 2008. "We see a lot of money pouring in from Russia."
Trump's campaign manager Paul Manafort also used to be a lobbyist for the pro-Russian president of Ukraine, who was ousted in 2014.
The Clinton campaign has accused Moscow of trying to meddle in the US election and help Trump. Adviser John Podesta pointed to a "bromance" between Trump and Putin.
"We don't have information right now about that, but what we have is a kind of bromance going on between Vladimir Putin and Trump which is distinct from this leak," Podesta said in an MSNBC interview about the email hack.
But Trump has dismissed the suggestion, tweeting: "The joke in town is that Russia leaked the disastrous DNC emails, which should never have been written (stupid), because Putin likes me."
Trump's senior policy adviser Paul Manafort called statements by the Clinton campaign "pretty desperate."
"It's a far reach, obviously," Manafort told reporters.
"To lead their convention with that tells me they really are trying to move away from what the issues are going to be in this campaign. It's pretty absurd."
Despite the denials, the controversy has shone a light on Trump's relationship with Russia and even has some asking whether Trump is Putin's puppet, and pointing to similarities between the two men, whose politics are both "mean, xenophobic, nationalistic and extreme".
As the presidential campaign hots up, Trump will now need to address concerns that his links to Russia won't influence his decisions in the Oval Office.