The CEO of the world's most successful social networking website was accused of at least two breaches of privacy in a series of articles run by BusinessInsider.com.
As part of a two-year investigation detailing the founding of Facebook, the magazine uncovered what it claimed was evidence of the hackings in 2004.
In the first instance, it said that, when Zuckerberg discovered that Harvard's student newspaper The Crimson was planning on running an article on him in 2004, he used reporters' Facebook logins to hack into their accounts.
In the second instance, the magazine claimed Zuckerberg hacked into the accounts of rivals at Harvard who accused him of stealing their idea for a social network. He then allegedly tried to sabotage the rival network they had set up.
Business Insider claimed that Zuckerberg learned The Crimson was planning to write an article on him when he was called in for an interview in 2004.The newspaper was investigating allegations by other Harvard students that Zuckerberg had stolen their social networking idea - allegations that are now well-documented and became the subject of a $65million legal suit.
In 2004, however, Facebook - which now boasts over 400million users around the world and is an incorporated company worth millions - was still just a network confined to Harvard students known as TheFacebook.com.
At the time, Zuckerberg was involved in a now well-publicised dispute with three other Harvard students who had originally asked him to help them create an online social network.
Business Insider chronicles the dispute in detail as part of its main article on the founding of Facebook.
The other Harvard students - Cameron Winklevoss, Tyler Winklevoss, and Divya Narendra - had accused Zuckerberg of intentionallly misleading them about his willingness to help them build their website, HarvardConnection.com.
They had approached the student newspaper, the Crimson, about their accusations.
On hearing their claims, Crimson reporters then spoke to Zuckerberg about the allegations, Business Insider said.
Zuckerberg was apparently able to convince the newspaper that he network he was building differed substantially to HarvardConnection.com, which he viewed primarily as a dating website. The newspaper pulled the story.
However after further claims emerged, Zuckerberg apparently became anxious that the paper would run a story on him after all.
Business Insider claimed he then told a friend how he had hacked into the accounts of Crimson staff.
He allegedly told the friend that he used TheFacebook.com to search for members who said they were Crimson staff.
Then, he allegedly examined a report of failed logins to see if any of the Crimson members had ever entered an incorrect password into TheFacebook.com.
In the instances where they had, Business Insider claimed that Zuckerberg said he tried using those incorrect passwords to access the Crimson members' Harvard email accounts.
In two instances, the magazine claimed, he succeeded - and was able to read emails between Crimson staff discussing the possibility of writing an article on the accusations surrounding him.
'In other words,' Business Insider claimed, 'Mark appears to have used private login data from TheFacebook to hack into the separate email accounts of some TheFacebook users'.
It would not be the only time that Zuckerberg breached privacy, Business Insider claimed.
In a separate article in the series, the magazine alleged that Zuckerberg had also hacked into his rivals at HarvardConnection.com - which, by May of 2004, had been renamed 'ConnectU'.
Although Facebook was already wildly popular by the summer of 2004 - reaching a million users by the fall - Zuckerberg, the magazine claimed, was still concerned about his competition.
Those concerns, it was alleged, led him to hack in to ConnectU's site and make changes to multiple user profiles - including one of its founders and the fellow student accusing him of stealing the ideas for Facebook, Cameron Winklevoss
Business Insider alleged that Zuckerberg created a fake account filled with fake information for Winklevoss.
It also alleged that he logged into the accounts of some ConnectU users and changed their privacy settings to invisible - apparently making it harder for people to find friends on the network.
Eventually, the magazine claimed, Zuckerberg deactivated at least 20 ConnectU accounts entirely.
Business Insider admitted it was not clear how Zuckerberg could have hacked into the ConnectU accounts.
When Facebook was approached about the allegations in the Business Insider articles, the company told Mail Online: 'We’re not going to debate the disgruntled litigants and anonymous sources who seek to rewrite Facebook’s early history or embarrass Mark Zuckerberg with dated allegations.
'The unquestioned fact is that since leaving Harvard for Silicon Valley nearly six years ago, Mark has led Facebook's growth from a college website to a global service playing an important role in the lives of over 400 million people.'
However the magazine also claimed that a source close to the company said it was the fallout from instances such as these - as well as the expensive litigation with ConnectU - that has shaped Facebook's current privacy policies.
Fears over privacy present one of Facebook's biggest challenges, with the company coming under fire from users almost every time it makes a change to its privacy policies.
After its investigation, Business Insider concluded that Zuckerberg had led his ConnectU rivals on regarding his own intentions of building a social network.
But the magazine said that, in light of the fact that Zuckerberg appeared to consider the two networks as two separate things, and that he had never signed a contract with Connect U, the $65million settlement eventually paid to ConnectU was over the top.
The alleged hackings detailed above, however, it claimed were far 'more troubling'.
The claims will be read with interest by the millions of Facebook users concerned about their privacy - but the full fallout still remains to be seen.
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