Ahmadinejad arrived on an Iran Air plane to a red carpet welcome by Vice President Khudayr al-Khuzaie, which was broadcast live on Iraqiya state television.
The Iranian president was invited by Iraqi President Jalal Talabani, but will be hosted by Khuzaie, as Talabani is abroad for medical treatment, Ali Mussawi, the Iraqi premier's spokesman, told AFP.
Ahmadinejad, whose term ends early next month, will visit the shrine of Imam Hussein in Karbala and that of Imam Ali in Najaf, two of the holiest sites in Shiite Islam, Mussawi said.