Following this attack, the users are being redirected to a page containing anti-America messages.
The page containing political messages shows an image of Arabic text overlaid on a green flag carrying the name of the third Shi'i Imam, Imam Husayn.
Twitter bosses have said they would start an investigation into what allowed the 'unplanned downtime' to take place.
It also included a poem in Persian, which said, "We shall strike if the leader orders, we shall lose our heads if the leader wishes."
Also included were the words, "Those that wage fight on the path of God win."
Soon after the images appeared Twitter went offline. About an hour later the site appeared to be working normally.
A post on the Twitter status blog said, "We are working to recovery (sic) from an unplanned downtime and will update more as we learn the cause of this outage."
Twitter has admitted that its Domain Name System (DNS) records had been "temporarily compromised". It said it was looking into what happened.
DNS acts as the address books for the internet. It tells browsing software where to find the computers hosting a particular webpage.
By attacking the DNS servers the hackers were able to re-direct Twitter users.
"These changes mean that when you or I type a website address into our browsers, we are directed not to the real website but to a second site, set up by the hackers, in this case the 'Iranian Cyber Army'," BBC News quoted Rik Ferguson from security firm Trend Micro as saying.
Ferguson said such attacks were typically a result of politically motivated hacking or 'hacktivism'.